Placing confidence limits on the molecular age of the human-chimpanzee divergence

Integrating Phylogenies with Chronology to Assemble the Tree of Life

Reconstructing the global Tree of Life necessitates computational approaches to integrate numerous molecular phylogenies with limited species overlap into a comprehensive supertree. Our survey of published literature shows that individual phylogenies are frequently restricted to specific taxonomic groups due to the expertise of investigators and molecular evolutionary considerations, resulting in any given species present in a minuscule fraction of phylogenies. We present a novel approach, called the chronological supertree algorithm (Chrono-STA), that can build a supertree of species from such data by using node ages in published molecular phylogenies scaled to time. Chrono-STA builds a supertree of organisms by integrating chronological data from molecular timetrees. It fundamentally differs from existing approaches that generate consensus phylogenies from gene trees with missing taxa, as Chrono-STA does not impute nodal distances, use a guide tree as a backbone, or reduce phylogenies to quartets. Analyses of simulated and empirical datasets show that Chrono-STA can combine taxonomically restricted timetrees with extremely limited species overlap. For such data, approaches that impute missing distances or assemble phylogenetic quartets did not perform well. We conclude that integrating phylogenies via temporal dimension enhances the accuracy of reconstructed supertrees that are also scaled to time.

Dating ancient splits in phylogenetic trees, with application to the human-Neanderthal split

BACKGROUND

We tackle the problem of estimating species TMRCAs (Time to Most Recent Common Ancestor), given a genome sequence from each species and a large known phylogenetic tree with a known structure (typically from one of the species). The number of transitions at each site from the first sequence to the other is assumed to be Poisson distributed, and only the parity of the number of transitions is observed. The detailed phylogenetic tree contains information about the transition rates in each site. We use this formulation to develop and analyze multiple estimators of the species' TMRCA. To test our methods, we use mtDNA substitution statistics from the well-established Phylotree as a baseline for data simulation such that the substitution rate per site mimics the real-world observed rates.

RESULTS

We evaluate our methods using simulated data and compare them to the Bayesian optimizing software BEAST2, showing that our proposed estimators are accurate for a wide range of TMRCAs and significantly outperform BEAST2. We then apply the proposed estimators on Neanderthal, Denisovan, and Chimpanzee mtDNA genomes to better estimate their TMRCA with modern humans and find that their TMRCA is substantially later, compared to values cited recently in the literature.

CONCLUSIONS

Our methods utilize the transition statistics from the entire known human mtDNA phylogenetic tree (Phylotree), eliminating the requirement to reconstruct a tree encompassing the specific sequences of interest. Moreover, they demonstrate notable improvement in both running speed and accuracy compared to BEAST2, particularly for earlier TMRCAs like the human-Chimpanzee split. Our results date the human - Neanderthal TMRCA to be [Formula: see text] years ago, considerably later than values cited in other recent studies.

Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human

Comparative analyses of MHC gene diversity and evolution across different species could offer valuable insights into the evolution of MHC genes. Intra- and inter-species sequence diversity and conservation of 12 classical major histocompatibility complex (MHC) class I genes from cattle, chimpanzees, pigs, and humans was analyzed using 20 representative allelic groups for each gene. The combined analysis of paralogous loci for each species revealed that intra-locus amino-acid sequence variations in the peptide-binding region (PBR) of MHC I genes did not differ significantly between species, ranging from 8.44% for SLA to 10.75% for BoLA class I genes. In contrast, intraspecies differences in the non-PBRs of these paralogous genes were more pronounced, varying from 4.59% for SLA to 16.89% for HLA. Interestingly, the Shannon diversity index and rate of nonsynonymous substitutions for PBR were significantly higher in SLA and BoLA than those in Patr and HLA. Analysis of peptide-binding pockets across all analyzed MHC class I genes of the four species indicated that pockets A and E showed the lowest and highest diversity, respectively. The estimated divergence times suggest that primate and artiodactyl MHC class I genes diverged 60.41 Mya, and BoLA and SLA genes diverged 35.34 Mya. These results offer new insights into the conservation and diversity of MHC class I genes in various mammalian species.

Genomic analysis reveals a new genus of Firetip skippers (Lepidoptera: Hesperiidae: Pyrrhopyginae)

We obtained whole genome shotgun sequence reads for a number of Firetip skippers (subfamily Pyrrhopyginae), including all known species from the genera Yanguna Watson, 1893 and Gunayan Mielke, 2002 and representative species of Pyrrhopyge Hübner, [1819]. Phylogenetic analysis of their protein-coding regions unexpectedly revealed that Yanguna tetricus Bell, 1931 was not monophyletic with the other species of Yanguna (type species Pyrrhopyga spatiosa Hewitson, 1870). Instead, Y. tetricus formed a phylogenetic lineage as ancient as other three genera in its clade (Pyrrhopyge, Yanguna and Gunayan) that rapidly diversified from their ancestor. Therefore a new genus, Guyanna Grishin, gen. n. (type species Yanguna tetricus), is proposed for this lineage. The specimen that we sequenced was the Y. tetricus holotype in the Natural History Museum, London, leaving no doubt that we are dealing with this species. Genomic sequencing and comparison of specimens from museum collections offers a powerful strategy to reveal unforeseen phylogenetic relationships, and sequencing of primary types ensures that the conclusions are accurate in terms of nomenclature.

Puberty initiates a unique stage of social learning and development prior to adulthood: Insights from studies of adolescence in wild chimpanzees

In humans, puberty initiates a period of rapid growth, change, and formative neurobehavioral development. Brain and behavior changes during this maturational window contribute to opportunities for social learning. Here we provide new insights into adolescence as a unique period of social learning and development by describing field studies of our closest living relatives, chimpanzees. Like humans, chimpanzees have a multiyear juvenile life stage between weaning and puberty onset followed by a multiyear adolescent life stage after pubertal onset but prior to socially-recognized adulthood. As they develop increasing autonomy from caregivers, adolescent chimpanzees explore and develop many different types of social relationships with a wide range of individuals in a highly flexible social environment. We describe how adolescent social motivations and experiences differ from those of juveniles and adults and expose adolescents to high levels of uncertainty, risk, and vulnerability, as well as opportunities for adaptive social learning. We discuss how these adolescent learning experiences may be shaped by early life and in turn shape varied adult social outcomes. We outline how future chimpanzee field research can contribute in new ways to a more integrative interdisciplinary understanding of adolescence as a developmental window of adaptive social learning and resilience.

Evolutionary Genetic Signatures of Selection on Bone-Related Variation within Human and Chimpanzee Populations

Bone strength and the incidence and severity of skeletal disorders vary significantly among human populations, due in part to underlying genetic differentiation. While clinical models predict that this variation is largely deleterious, natural population variation unrelated to disease can go unnoticed, altering our perception of how natural selection has shaped bone morphologies over deep and recent time periods. Here, we conduct the first comparative population-based genetic analysis of the main bone structural protein gene, collagen type I α 1 (COL1A1), in clinical and 1000 Genomes Project datasets in humans, and in natural populations of chimpanzees. Contrary to predictions from clinical studies, we reveal abundant COL1A1 amino acid variation, predicted to have little association with disease in the natural population. We also find signatures of positive selection associated with intron haplotype structure, linkage disequilibrium, and population differentiation in regions of known gene expression regulation in humans and chimpanzees. These results recall how recent and deep evolutionary regimes can be linked, in that bone morphology differences that developed among vertebrates over 450 million years of evolution are the result of positive selection on subtle type I collagen functional variation segregating within populations over time.

Estimating origination times from the early hominin fossil record

The age of the earliest recovered fossil evidence of a hominin taxon is all too often equated with that taxon's origination. However, the earliest known fossil record nearly always postdates, sometimes by a substantial period of time, the true origination of a taxon. Here we evaluate the first appearance records of the earliest potential hominins (Sahelanthropus, Ardipithecus, Orrorin), as well as of the genera Australopithecus, Homo, and Paranthropus, to illustrate the considerable uncertainty regarding the actual timing of origin of these taxa. By placing confidence intervals on the first appearance records of early hominin taxa, we can better evaluate patterns of hominin diversity, turnover, and potential correlations with climatic and environmental changes.

Reproductive Character Displacement Drives Diversification of Male Courtship Songs in Drosophila

AbstractMale secondary sexual traits are one of the most striking and diverse features of the animal kingdom. While these traits are often thought to evolve via sexual selection, many questions remain about their patterns of diversification and their role in speciation. To address these questions, I performed a comparative study of precopulatory male courtship songs of 119 Drosophila species across 10 distinct species groups. I related song divergence to genetic distances, geographic relationships, and sexual isolation between species. On the basis of pairwise Euclidean song distances, species groups typically retained their phylogenetic signal while species within groups diverged five times more in sympatry relative to allopatry, producing a pattern of reproductive character displacement. This occurred despite similar genetic distances in allopatry and sympatry, was exaggerated among younger species pairs, and was driven primarily by the parameter interpulse interval. While sexual isolation in sympatry was high even with low song divergence, these variables were correlated with each other and with increased divergence of female mating preferences in sympatry. The widespread pattern of character displacement implies that allopatric divergence due to processes like sexual selection are very slow relative to sympatric processes such as reinforcement and reproductive interference in driving song diversification across Drosophila.

The nonhuman primate neuroimaging and neuroanatomy project

Multi-modal neuroimaging projects such as the Human Connectome Project (HCP) and UK Biobank are advancing our understanding of human brain architecture, function, connectivity, and their variability across individuals using high-quality non-invasive data from many subjects. Such efforts depend upon the accuracy of non-invasive brain imaging measures. However, 'ground truth' validation of connectivity using invasive tracers is not feasible in humans. Studies using nonhuman primates (NHPs) enable comparisons between invasive and non-invasive measures, including exploration of how "functional connectivity" from fMRI and "tractographic connectivity" from diffusion MRI compare with long-distance connections measured using tract tracing. Our NonHuman Primate Neuroimaging & Neuroanatomy Project (NHP_NNP) is an international effort (6 laboratories in 5 countries) to: (i) acquire and analyze high-quality multi-modal brain imaging data of macaque and marmoset monkeys using protocols and methods adapted from the HCP; (ii) acquire quantitative invasive tract-tracing data for cortical and subcortical projections to cortical areas; and (iii) map the distributions of different brain cell types with immunocytochemical stains to better define brain areal boundaries. We are acquiring high-resolution structural, functional, and diffusion MRI data together with behavioral measures from over 100 individual macaques and marmosets in order to generate non-invasive measures of brain architecture such as myelin and cortical thickness maps, as well as functional and diffusion tractography-based connectomes. We are using classical and next-generation anatomical tracers to generate quantitative connectivity maps based on brain-wide counting of labeled cortical and subcortical neurons, providing ground truth measures of connectivity. Advanced statistical modeling techniques address the consistency of both kinds of data across individuals, allowing comparison of tracer-based and non-invasive MRI-based connectivity measures. We aim to develop improved cortical and subcortical areal atlases by combining histological and imaging methods. Finally, we are collecting genetic and sociality-associated behavioral data in all animals in an effort to understand how genetic variation shapes the connectome and behavior.

Quest for the Best Evolutionary Model

In the early 1980s, DNA sequencing became a routine and the increasing computing power opened the door to reconstruct molecular phylogenies using probabilistic approaches. DNA sequence alignments provided a large number of positions containing phylogenetic information, which could be extracted using explicit statistical models that described the mutation process using appropriate parameters. Consequently, an active quest started for building increasingly improved (more realistic) statistical models of nucleotide substitution. The simplest model assumed that nucleotide frequencies were in equilibrium and one single category of substitutions. Subsequent models allowed either unequal nucleotide frequencies or separate rates for transitions and transversions. The HKY85 model (Hasegawa et al. in J Mol Evol 22:160, 1985) combined elegantly both options into a single model, which became one of the most useful ones and has been the choice in many molecular phylogenetic studies ever since. The use of improved substitution models such as HKY85 allows reconstructing more accurate and reliable phylogenies, which in turn provide robust frameworks for understanding how biological diversity evolved and for performing a wealth of comparative studies in different disciplines such as ecology, biogeography, developmental biology, biochemistry, genomics, epidemiology, and biomedicine.

Flexible Mixture Model Approaches That Accommodate Footprint Size Variability for Robust Detection of Balancing Selection

Long-term balancing selection typically leaves narrow footprints of increased genetic diversity, and therefore most detection approaches only achieve optimal performances when sufficiently small genomic regions (i.e., windows) are examined. Such methods are sensitive to window sizes and suffer substantial losses in power when windows are large. Here, we employ mixture models to construct a set of five composite likelihood ratio test statistics, which we collectively term B statistics. These statistics are agnostic to window sizes and can operate on diverse forms of input data. Through simulations, we show that they exhibit comparable power to the best-performing current methods, and retain substantially high power regardless of window sizes. They also display considerable robustness to high mutation rates and uneven recombination landscapes, as well as an array of other common confounding scenarios. Moreover, we applied a specific version of the B statistics, termed B2, to a human population-genomic data set and recovered many top candidates from prior studies, including the then-uncharacterized STPG2 and CCDC169-SOHLH2, both of which are related to gamete functions. We further applied B2 on a bonobo population-genomic data set. In addition to the MHC-DQ genes, we uncovered several novel candidate genes, such as KLRD1, involved in viral defense, and SCN9A, associated with pain perception. Finally, we show that our methods can be extended to account for multiallelic balancing selection and integrated the set of statistics into open-source software named BalLeRMix for future applications by the scientific community.

Emotional Voice Intonation: A Communication Code at the Origins of Speech Processing and Word-Meaning Associations?

The aim of the present work is to investigate the facilitating effect of vocal emotional intonation on the evolution of the following processes involved in language: (a) identifying and producing phonemes, (b) processing compositional rules underlying vocal utterances, and (c) associating vocal utterances with meanings. To this end, firstly, I examine research on the presence of these abilities in animals, and the biologically ancient nature of emotional vocalizations. Secondly, I review research attesting to the facilitating effect of emotional voice intonation on these abilities in humans. Thirdly, building on these studies in animals and humans, and through taking an evolutionary perspective, I provide insights for future empirical work on the facilitating effect of emotional intonation on these three processes in animals and preverbal humans. In this work, I highlight the importance of a comparative approach to investigate language evolution empirically. This review supports Darwin’s hypothesis, according to which the ability to express emotions through voice modulation was a key step in the evolution of spoken language.

Evolution of Speech: Anatomy and Control

Purpose This article critically reviews work on the evolution of speech in the context of motor control. It presents a brief introduction to the field of language evolution, of which the study of the evolution of speech is an integral component, and argues why taking the evolutionary perspective is useful. It then proceeds to review different methods of studying evolutionary questions: comparative research, experimental and observational research, and computer and mathematical modeling. Conclusions On the basis of comparative analysis of related species (specifically, other great apes) and on the basis of theoretical results, this article argues that adaptations for speech must have evolved gradually and that it is likely that speech motor control is one of the key aspects that has undergone observable selection related to speech, because, in this area, all the necessary precursors are present in closely related species. This implies that it must be possible to find empirical evidence for how speech evolved in the area of speech motor control. However, such research is only in its infancy at the present moment.

The evolution of male and female mating preferences in Drosophila speciation

The relative importance of male and female mating preferences in causing sexual isolation between species remains a major unresolved question in speciation. Despite previous work showing that male courtship bias and/or female copulation bias for conspecifics occur in many taxa, the present study is one of the first large-scale works to study their relative divergence. To achieve this, we used data from the literature and present experiments across 66 Drosophila species pairs. Our results revealed that male and female mate preferences are both ubiquitous in Drosophila but evolved largely independently, suggesting different underlying evolutionary and genetic mechanisms. Moreover, their relative divergence strongly depends on the geographical relationship of species. Between allopatric species, male courtship and female copulation preferences diverged at very similar rates, evolving approximately linearly with time of divergence. In sharp contrast, between sympatric species pairs, female preferences diverged much more rapidly than male preferences and were the only drivers of enhanced sexual isolation in sympatry and Reproductive Character Displacement (RCD). Not only does this result suggest that females are primarily responsible for such processes as reinforcement, but it also implies that evolved female preferences may reduce selection for further divergence of male courtship preferences in sympatry.

Detection of Shared Balancing Selection in the Absence of Trans-Species Polymorphism

Trans-species polymorphism has been widely used as a key sign of long-term balancing selection across multiple species. However, such sites are often rare in the genome and could result from mutational processes or technical artifacts. Few methods are yet available to specifically detect footprints of trans-species balancing selection without using trans-species polymorphic sites. In this study, we develop summary- and model-based approaches that are each specifically tailored to uncover regions of long-term balancing selection shared by a set of species by using genomic patterns of intraspecific polymorphism and interspecific fixed differences. We demonstrate that our trans-species statistics have substantially higher power than single-species approaches to detect footprints of trans-species balancing selection, and are robust to those that do not affect all tested species. We further apply our model-based methods to human and chimpanzee whole-genome sequencing data. In addition to the previously established major histocompatibility complex and malaria resistance-associated FREM3/GYPE regions, we also find outstanding genomic regions involved in barrier integrity and innate immunity, such as the GRIK1/CLDN17 intergenic region, and the SLC35F1 and ABCA13 genes. Our findings not only echo the significance of pathogen defense but also reveal novel candidates in maintaining balanced polymorphisms across human and chimpanzee lineages. Finally, we show that these trans-species statistics can be applied to and work well for an arbitrary number of species, and integrate them into open-source software packages for ease of use by the scientific community.

The Cultural Brain Hypothesis: How culture drives brain expansion, sociality, and life history

In the last few million years, the hominin brain more than tripled in size. Comparisons across evolutionary lineages suggest that this expansion may be part of a broader trend toward larger, more complex brains in many taxa. Efforts to understand the evolutionary forces driving brain expansion have focused on climatic, ecological, and social factors. Here, building on existing research on learning, we analytically and computationally model the predictions of two closely related hypotheses: The Cultural Brain Hypothesis and the Cumulative Cultural Brain Hypothesis. The Cultural Brain Hypothesis posits that brains have been selected for their ability to store and manage information, acquired through asocial or social learning. The model of the Cultural Brain Hypothesis reveals relationships between brain size, group size, innovation, social learning, mating structures, and the length of the juvenile period that are supported by the existing empirical literature. From this model, we derive a set of predictions-the Cumulative Cultural Brain Hypothesis-for the conditions that favor an autocatalytic take-off characteristic of human evolution. This narrow evolutionary pathway, created by cumulative cultural evolution, may help explain the rapid expansion of human brains and other aspects of our species' life history and psychology.

Relationships Between Gastrointestinal Parasite Infections and the Fecal Microbiome in Free-Ranging Western Lowland Gorillas

Relationships between gastrointestinal parasites (GIPs) and the gastrointestinal microbiome (GIM) are widely discussed topics across mammalian species due to their possible impact on the host's health. GIPs may change the environment determining alterations in GIM composition. We evaluated the associations between GIP infections and fecal microbiome composition in two habituated and two unhabituated groups of wild western lowland gorillas (Gorilla g. gorilla) from Dzanga Sangha Protected Areas, Central African Republic. We examined 43 fecal samples for GIPs and quantified strongylid nematodes. We characterized fecal microbiome composition through 454 pyrosequencing of the V1-V3 region of the bacterial 16S rRNA gene. Entamoeba spp. infections were associated with significant differences in abundances of bacterial taxa that likely play important roles in nutrition and metabolism for the host, besides being characteristic members of the gorilla gut microbiome. We did not observe any relationships between relative abundances of several bacterial taxa and strongylid egg counts. Based on our findings, we suggest that there is a significant relationship between fecal microbiome and Entamoeba infection in wild gorillas. This study contributes to the overall knowledge about factors involved in modulating GIM communities in great apes.

Toward a consensus on SNP and STR mutation rates on the human Y-chromosome

The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate. The current estimate of the "envelope rate" is 0.75-0.89 substitutions per billion base pairs per year. The available Y-SNP mutation rates can be applied to high-coverage data from the entire X-degenerate region, but other datasets may demand recalibrated rates. While a consensus on Y-SNP rates is approaching, the debate on Y-STR rates has continued for two decades, because multiple genealogical rates were consistent with each other but three times faster than the single evolutionary estimate. Applying Y-SNP and Y-STR rates to the same haplogroups recently helped to clarify the issue. Genealogical and evolutionary STR rates typically provide lower and upper bounds of the "true" (SNP-based) age. The genealogical rate often-but not always-works well for haplogroups less than 7000 years old. The evolutionary rate, although calibrated using recent events, inflates ages of young haplogroups and deflates the age of the entire Y-chromosomal tree, but often provides reasonable estimates for intermediate ages (old haplogroups). Future rate estimates and accumulating case studies should further clarify the Y-SNP rates.

Copy Number Variation in TAS2R Bitter Taste Receptor Genes: Structure, Origin, and Population Genetics

Bitter taste receptor genes (TAS2Rs) harbor extensive diversity, which is broadly distributed across human populations and strongly associated with taste response phenotypes. The majority of TAS2R variation is composed of single-nucleotide polymorphisms. However, 2 closely positioned loci at 12p13, TAS2R43 and -45, harbor high-frequency deletion (Δ) alleles in which genomic segments are absent, resulting in copy number variation (CNV). To resolve their chromosomal structure and organization, we generated maps using long-range contig alignments and local sequencing across the TAS2R43-45 region. These revealed that the deletion alleles (43Δ and 45Δ) are 37.8 and 32.2kb in length, respectively and span the complete coding region of each gene (~1kb) along with extensive up- and downstream flanking sequence, producing separate CNVs at the 2 loci. Comparisons with a chimpanzee genome, which contained intact homologs of TAS2R43, -45, and nearby TAS2Rs, indicated that the deletions evolved recently, through unequal recombination in a cluster of closely related loci. Population genetic analyses in 946 subjects from 52 worldwide populations revealed that copy number ranged from 0 to 2 at both TAS2R43 and TAS2R45, with 43Δ and 45Δ occurring at high global frequencies (0.33 and 0.18). Estimated recombination rates between the loci were low (ρ = 2.7×10(-4); r = 6.6×10(-9)) and linkage disequilibrium was high (D' = 1.0), consistent with their adjacent genomic positioning and recent origin. Geographic variation pointed to an African origin for the deletions. However, no signatures of natural selection were found in population structure or integrated haplotype scores spanning the region, suggesting that patterns of diversity at TAS2R43 and -45 are primarily due to genetic drift.

Comparison of predicted and actual consequences of missense mutations

Each person's genome sequence has thousands of missense variants. Practical interpretation of their functional significance must rely on computational inferences in the absence of exhaustive experimental measurements. Here we analyzed the efficacy of these inferences in 33 de novo missense mutations revealed by sequencing in first-generation progeny of N-ethyl-N-nitrosourea-treated mice, involving 23 essential immune system genes. PolyPhen2, SIFT, MutationAssessor, Panther, CADD, and Condel were used to predict each mutation's functional importance, whereas the actual effect was measured by breeding and testing homozygotes for the expected in vivo loss-of-function phenotype. Only 20% of mutations predicted to be deleterious by PolyPhen2 (and 15% by CADD) showed a discernible phenotype in individual homozygotes. Half of all possible missense mutations in the same 23 immune genes were predicted to be deleterious, and most of these appear to become subject to purifying selection because few persist between separate mouse substrains, rodents, or primates. Because defects in immune genes could be phenotypically masked in vivo by compensation and environment, we compared inferences by the same tools with the in vitro phenotype of all 2,314 possible missense variants in TP53; 42% of mutations predicted by PolyPhen2 to be deleterious (and 45% by CADD) had little measurable consequence for TP53-promoted transcription. We conclude that for de novo or low-frequency missense mutations found by genome sequencing, half those inferred as deleterious correspond to nearly neutral mutations that have little impact on the clinical phenotype of individual cases but will nevertheless become subject to purifying selection.

Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

Is the prefrontal cortex especially enlarged in the human brain allometric relations and remapping factors

There has been no agreement as to whether the prefrontal cortex is especially enlarged in the human brain. To answer this question, we analyzed the only two datasets that provide information on total prefrontal cortex volume based on cytoarchitectonic criteria. One delineated the prefrontal cortex proper on the basis of cytoarchitectonic criteria; the other used a proxy of the prefrontal cortex based on a cytoarchitectonic delineation of the frontal lobe. To investigate whether all cortical association areas, including the prefrontal cortex, are enlarged in the human brain, we scaled the different areas to a common reference, the primary visual cortex. To investigate whether the prefrontal cortex is more enlarged than other association areas, we scaled it relative to its inputs from and outputs to other nonprimary areas. We carried out separate regression analyses using different data samples as a predictive baseline group: data for monkeys alone informs us on whether great apes are different from monkeys; data for all non-human anthropoids, including great apes, informs us on whether humans are different from all other primates. The analyses show that the value for the human prefrontal cortex is greater than expected, and that this is true even when data for the great apes are included in the analysis. They also show that the chimpanzee prefrontal cortex is greater than expected for a monkey with a similar sized cortex. We discuss possible functional consequences.

Evaluating the Y chromosomal timescale in human demographic and lineage dating

Y chromosome is a superb tool for inferring human evolution and recent demographic history from a paternal perspective. However, Y chromosomal substitution rates obtained using different modes of calibration vary considerably, and have produced disparate reconstructions of human history. Here, we discuss how substitution rate and date estimates are affected by the choice of different calibration points. We argue that most Y chromosomal substitution rates calculated to date have shortcomings, including a reliance on the ambiguous human-chimpanzee divergence time, insufficient sampling of deep-rooting pedigrees, and using inappropriate founding migrations, although the rates obtained from a single pedigree or calibrated with the peopling of the Americas seem plausible. We highlight the need for using more deep-rooting pedigrees and ancient genomes with reliable dates to improve the rate estimation.

Evolutionary origins of human herpes simplex viruses 1 and 2

Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this pattern of virus-host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes. Humans are the only primate species known to be infected with two distinct herpes simplex viruses: HSV-1 and HSV-2. Human herpes simplex viruses are ubiquitous, with over two-thirds of the human population infected by at least one virus. Here, we investigated whether the additional human simplex virus is the result of ancient viral lineage duplication or cross-species transmission. We found that standard phylogenetic models of nucleotide substitution are inadequate for distinguishing among these competing hypotheses; the extent of synonymous substitutions causes a substantial underestimation of the lengths of some of the branches in the phylogeny, consistent with observations in other viruses (e.g., avian influenza, Ebola, and coronaviruses). To more accurately estimate ancient viral divergence times, we applied a branch-site random effects likelihood model of molecular evolution that allows the strength of natural selection to vary across both the viral phylogeny and the gene alignment. This selection-informed model favored a scenario in which HSV-1 is the result of ancient codivergence and HSV-2 arose from a cross-species transmission event from the ancestor of modern chimpanzees to an extinct Homo precursor of modern humans, around 1.6 Ma. These results provide a new framework for understanding human herpes simplex virus evolution and demonstrate the importance of using selection-informed models of sequence evolution when investigating viral origin hypotheses.

A model-based approach for identifying signatures of ancient balancing selection in genetic data

While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated methods for identifying sites under balancing selection. Here we develop two composite likelihood ratio tests for detecting balancing selection. Using simulations, we show that these methods outperform competing methods under a variety of assumptions and demographic models. We apply the new methods to whole-genome human data, and find a number of previously-identified loci with strong evidence of balancing selection, including several HLA genes. Additionally, we find evidence for many novel candidates, the strongest of which is FANK1, an imprinted gene that suppresses apoptosis, is expressed during meiosis in males, and displays marginal signs of segregation distortion. We hypothesize that balancing selection acts on this locus to stabilize the segregation distortion and negative fitness effects of the distorter allele. Thus, our methods are able to reproduce many previously-hypothesized signals of balancing selection, as well as discover novel interesting candidates.

In the past, balancing selection was a topic of great theoretical interest that received much attention. However, there has been little focus toward developing methods to identify regions of the genome that are under balancing selection. In this article, we present the first set of likelihood-based methods that explicitly model the spatial distribution of polymorphism expected near a site under long-term balancing selection. Simulation results show that our methods outperform commonly-used summary statistics for identifying regions under balancing selection. Finally, we performed a scan for balancing selection in Africans and Europeans using our new methods and identified a gene called FANK1 as our top candidate outside the HLA region. We hypothesize that the maintenance of polymorphism at FANK1 is the result of segregation distortion.

Quantifying the effects of anagenetic and cladogenetic evolution

An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation between species and attribute the proportion of change to each type. I discuss results of parameter estimation of Hominoid body size in this light. I derive mathematical formulae related to this problem, the probability generating functions of the number of speciation events along a randomly drawn lineage and from the most recent common ancestor of two randomly chosen tip species for a conditioned Yule tree. Additionally I obtain in closed form the variance of the distance from the root to the most recent common ancestor of two randomly chosen tip species.

Genes with a large intronic burden show greater evolutionary conservation on the protein level

BACKGROUND

The existence of introns in eukaryotic genes is believed to provide an evolutionary advantage by increasing protein diversity through exon shuffling and alternative splicing. However, this eukaryotic feature is associated with the necessity of exclusion of intronic sequences, which requires considerable energy expenditure and can lead to splicing errors. The relationship between intronic burden and evolution is poorly understood. The goal of this study was to analyze the relationship between the intronic burden and the level of evolutionary conservation of the gene.

RESULTS

We found a positive correlation between the level of evolutionary conservation of a gene and its intronic burden. The level of evolutionary conservation was estimated using the conservation index (CI). The CI value was determined on the basis of the most distant ortholog of the human protein sequence and ranged from 0 (the gene was unique to the human genome) to 9 (an ortholog of the human gene was detected in plants). In multivariable model, both the number of introns and total intron size remained significant predictors of CI. We also found that the number of alternative splice variants was positively correlated with CI.The expression level of a gene was negatively correlated with the number of introns and total size of intronic region. Genes with a greater intronic burden had lower density of missense and nonsense mutations in the coding regions of the gene, which suggests that they are under a stronger pressure from purifying selection.

CONCLUSIONS

We identified a positive association between intronic burden and CI. One of the possible explanations of this is the idea of a cost-benefits balance. Evolutionarily conserved (functionally important) genes can "afford" the negative consequences of maintaining multiple introns because these consequences are outweighed by the benefit of maintaining the gene. Evolutionarily conserved and functionally important genes may use introns to create novel splice variants to tune the gene function to developmental stage and tissue type.

Molecular phylogeography of a human autosomal skin color locus under natural selection

Divergent natural selection caused by differences in solar exposure has resulted in distinctive variations in skin color between human populations. The derived light skin color allele of the SLC24A5 gene, A111T, predominates in populations of Western Eurasian ancestry. To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin. The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.

A New Approach for Sequence Analysis

Understanding the structure-function relationship of proteins offers the key to biological processes, and can offer knowledge for better investigation of matters with widespread impact, such as pathological disease and drug intervention. This relationship is dictated at the simplest level by the primary protein sequence. Since useful structures and functions are conserved within biology, a sequence with known structure-function relationship can be compared to related sequences to aid in novel structure-function prediction. Sequence analysis provides a means for suggesting evolutionary relationships, and inferring structural or functional similarity. It is crucial to consider these parameters while comparing sequences as they influence both the algorithms used and the implications of the results. For example, proteins that are closely related on an evolutionary time scale may have very similar structure, but entirely different functions. In contrast, proteins which have undergone convergent evolution may have dissimilar primary structure, but perform similar functions. This chapter details how the aspects of evolution, structure, and function can be taken into account when performing sequence analysis, and proposes an expansion on traditional approaches resulting in direct improvement of said analysis. This model is applied to a case study in the prestin protein and shows that the proposed approach provides a better understanding of input and output and can improve the performance of sequence analysis by means of motif detection software.

Shared human-chimpanzee pattern of perinatal femoral shaft morphology and its implications for the evolution of hominin locomotor adaptations

BACKGROUND

Acquisition of bipedality is a hallmark of human evolution. How bipedality evolved from great ape-like locomotor behaviors, however, is still highly debated. This is mainly because it is difficult to infer locomotor function, and even more so locomotor kinematics, from fossil hominin long bones. Structure-function relationships are complex, as long bone morphology reflects phyletic history, developmental programs, and loading history during an individual's lifetime. Here we discriminate between these factors by investigating the morphology of long bones in fetal and neonate great apes and humans, before the onset of locomotion.

METHODOLOGY/PRINCIPAL FINDINGS

Comparative morphometric analysis of the femoral diaphysis indicates that its morphology reflects phyletic relationships between hominoid taxa to a greater extent than taxon-specific locomotor adaptations. Diaphyseal morphology in humans and chimpanzees exhibits several shared-derived features, despite substantial differences in locomotor adaptations. Orangutan and gorilla morphologies are largely similar, and likely represent the primitive hominoid state.

CONCLUSIONS/SIGNIFICANCE

These findings are compatible with two possible evolutionary scenarios. Diaphyseal morphology may reflect retained adaptive traits of ancestral taxa, hence human-chimpanzee shared-derived features may be indicative of the locomotor behavior of our last common ancestor. Alternatively, diaphyseal morphology might reflect evolution by genetic drift (neutral evolution) rather than selection, and might thus be more informative about phyletic relationships between taxa than about locomotor adaptations. Both scenarios are consistent with the hypothesis that knuckle-walking in chimpanzees and gorillas resulted from convergent evolution, and that the evolution of human bipedality is unrelated to extant great ape locomotor specializations.

Unexpectedly many extinct hominins

Recent studies indicate that Neanderthal and Denisova hominins may have been separate species, while debate continues on the status of Homo floresiensis. The decade-long debate between "splitters," who recognize over 20 hominin species, and "lumpers," who maintain that all these fossils belong to just a few lineages, illustrates that we do not know how many extinct hominin species to expect. Here, we present probability distributions for the number of speciation events and the number of contemporary species along a branch of a phylogeny. With estimates of hominin speciation and extincton rates, we then show that the expected total number of extinct hominin species is 8, but may be as high as 27. We also show that it is highly unlikely that three very recent species disappeared due to natural, background extinction. This may indicate that human-like remains are too easily considered distinct species. Otherwise, the evidence suggesting that Neanderthal and the Denisova hominin represent distinct species implies a recent wave of extinctions, ostensibly driven by the only survivor, H. sapiens.

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.

Newly evolved genes: moving from comparative genomics to functional studies in model systems. How important is genetic novelty for species adaptation and diversification?

Genes are gained and lost over the course of evolution. A recent study found that over 1,800 new genes have appeared during primate evolution and that an unexpectedly high proportion of these genes are expressed in the human brain. But what are the molecular functions of newly evolved genes and what is their impact on an organism's fitness? The acquisition of new genes may provide a rich source of genetic diversity that fuels evolutionary innovation. Although gene manipulation experiments are not feasible in humans, studies in model organisms, such as Drosophila melanogaster, have shown that new genes can quickly become integrated into genetic networks and become essential for survival or fertility. Future studies of new genes, especially chimeric genes, and their functions will help determine the role of genetic novelty in the adaptation and diversification of species.

A trans-specific polymorphism in ZC3HAV1 is maintained by long-standing balancing selection and may confer susceptibility to multiple sclerosis

The human ZC3HAV1 gene encodes an antiviral protein. The longest splicing isoform of ZC3HAV1 contains a C-terminal PARP-like domain, which has evolved under positive selection in primates. We analyzed the evolutionary history of this same domain in humans and in Pan troglodytes. We identified two variants that segregate in both humans and chimpanzees; one of them (rs3735007) does not occur at a hypermutable site and accounts for a nonsynonymous substitution (Thr851Ile). The probability that the two trans-specific polymorphisms have occurred independently in the two lineages was estimated to be low (P = 0.0054), suggesting that at least one of them has arisen before speciation and has been maintained by selection. Population genetic analyses in humans indicated that the region surrounding the shared variants displays strong evidences of long-standing balancing selection. Selection signatures were also observed in a chimpanzee population sample. Inspection of 1000 Genomes data confirmed these findings but indicated that search for selection signatures using low-coverage whole-genome data may need masking of repetitive sequences. A case–control study of more than 1,000 individuals from mainland Italy indicated that the Thr851Ile SNP is significantly associated with susceptibility to multiple sclerosis (MS) (odds ratio [OR] = 1.47, 95% confidence intervals [CI]: 1.08–1.99, P = 0.011). This finding was confirmed in a larger sample of 4,416 Sardinians cases/controls (OR = 1.18, 95% CI: 1.037–1.344, P = 0.011), but not in a population from Belgium. We provide one of the first instances of human/chimpanzee trans-specific coding variant located outside the major histocompatibility complex region. The selective pressure is likely to be virus driven; in modern populations, this variant associates with susceptibility to MS, possibly via the interaction with environmental factors.

Is speciation accompanied by rapid evolution? Insights from comparing reproductive and nonreproductive transcriptomes in Drosophila

The tempo and mode of evolutionary change during speciation have remained contentious until recently. While much of the evidence claiming speciation is an abrupt and rapid process comes from fossil data, recent molecular phylogenetics show that the background of gradual evolution is often broken by accelerated rates of molecular evolution during speciation. However, what kinds of genes affect or are affected by speciation remains unexplored. Our analysis of 4843 protein-coding genes in five species of the Drosophila melanogaster subgroup shows that while ~70% of genes follow clock-like evolution, between 17-19.67% of loci show signatures of accelerated rates of evolution in recently formed species. These genes show 2-3-fold higher rates of substitution in recently diverged species compared to older species. This fraction of loci affects a diverse range of functions. Only a small proportion of reproductive genes experience speciation-related accelerated changes but many sex-and -reproduction related genes show an interesting pattern of persistent rapid evolution suggesting that sex-and-reproduction related genes are under constant selective pressures. The identification of loci associated with accelerated evolution allows us to address the mechanisms of rapid evolution and speciation, which in our study appears to be a combination of both selection and rapid demographical changes.

Patterns of genetic variation within and between Gibbon species

Gibbons are small, arboreal, highly endangered apes that are understudied compared with other hominoids. At present, there are four recognized genera and approximately 17 species, all likely to have diverged from each other within the last 5-6 My. Although the gibbon phylogeny has been investigated using various approaches (i.e., vocalization, morphology, mitochondrial DNA, karyotype, etc.), the precise taxonomic relationships are still highly debated. Here, we present the first survey of nuclear sequence variation within and between gibbon species with the goal of estimating basic population genetic parameters. We gathered ~60 kb of sequence data from a panel of 19 gibbons representing nine species and all four genera. We observe high levels of nucleotide diversity within species, indicative of large historical population sizes. In addition, we find low levels of genetic differentiation between species within a genus comparable to what has been estimated for human populations. This is likely due to ongoing or episodic gene flow between species, and we estimate a migration rate between Nomascus leucogenys and N. gabriellae of roughly one migrant every two generations. Together, our findings suggest that gibbons have had a complex demographic history involving hybridization or mixing between diverged populations.

Recombination-suppression: how many mechanisms for chromosomal speciation?

Over the past decade several theoretical and empirical studies have revived interest in the role of chromosomes in speciation. The resulting models do not suffer from the problems experienced by previously proposed mechanisms of chromosomal speciation, because they invoke suppression of recombination rather than a reduction in the fitness of heterokaryotypes as their core process. However, they are not free from difficulties. The evidence for recombination-suppression models is discussed here. The general conclusion is that a consensus opinion on which models best describe the real-world situation is currently unlikely because of an inability of the available empirical evidence to fully distinguish between them, which may be due in part to a lack of exclusivity. I argue that future work should take this lack of exclusivity into account. Resolving the biogeography of speciation is also suggested in order to tell the various models apart. Further study is needed which focuses on confirming the operation of individual elements of the various models, rather than attempting to validate any single mechanism as a whole.

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human-chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1-1.5, 1.1-0.76 and 0.25-0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.

Genome digging: insight into the mitochondrial genome of Homo

BACKGROUND

A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt) on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1) into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split.

PRINCIPAL FINDINGS

Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2) with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000-485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively.

CONCLUSIONS

This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d(N)/d(S) dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective population size and possessed genetic diversity comparable with those of chimpanzee and gorilla.

Detecting gene duplications in the human lineage

Gene duplications represent an important class of evolutionary events that is likely to have contributed to the unique human phenotype in the short evolutionary time since the human-chimpanzee divergence. With the availability of both human and chimpanzee genome drafts in high coverage re-sequencing assemblies and the high annotation quality of most human genes, it should now be possible to identify all human lineage-specific gene duplication events (human inparalogues) and a few pioneering studies have attempted to do that. However, the different levels of coverage in the human and chimpanzee's genomes assemblies, and the differing levels of gene annotation, have led to problematic assumptions and oversimplifications in the algorithms and the datasets used to detect human lineage-specific gene duplications. In this study, we have developed a set of bioinformatic tools to overcome a number of the conceptual problems that are prevalent in previous studies and have collected a reliable and representative set of human inparalogues.

Novel intron markers to study the phylogeny of closely related mammalian species

BACKGROUND

Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies.

RESULTS

In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals.

CONCLUSIONS

We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification and enough variability in most species, indicating that this marker set can be very helpful in multilocus phylogenetics of mammals. Due to the lower variability and stronger stochasticity of nuclear markers with respect to mitochondrial genes, studies should be designed to make use of several markers like the ones designed here.