Evolutionary ontogenetic aspects of pathogenetics of chronic human diseases

This article is a review of scientific publications, in which issues of pathogenetics of multifactorial diseases (MFDs) are considered from the viewpoint of evolution and ontogeny. Concepts explaining significance of evolutionary processes in the formation of genetic architecture of human chronic diseases (“thrifty” genomes and phenotypes, “drifty genes,” decanalization) are analyzed. The roles of natural selection and genetic drift in the formation of hereditary diversity of genes for susceptibility to MFDs are considered. The modern concept of “disease ontogeny” (somatic mosaicism, loss of heterozygosity, paradominant inheritance, epigenetic variability) is discussed. It is demonstrated that the evolutionary and ontogenetic approaches to analysis of genimuc and other “-omic” data are essential for understanding the biology of diseases.     

Experimental histology and the problems of the evolution of tissues

Trends in modern histology have been reviewed. The role of evolutionary concepts (hypotheses) in analysis of experimental data has been stressed. Several problems of onto- and phylogenesis of hemopoiesis have been discussed. They include evolution of structure of hemopoietic system; origin of fibroblasts and correlation of hemal (mobile) and desmal (fixed) mesenchymal cells; immunological approaches to studies of evolution of hemopoietic cell.     

植物miRNA的进化

鉴于miRNA在植物基因表达调控中的重要作用, 人们已经开展对植物miRNA的预测、鉴定、功能和进化等方面的研究。随着许多模式植物基因组测序的完成, miRNA的基因组学和进化信息的整合为miRNA的起源和进化研究提供了越来越多的证据和假说, 然而尚未见关于植物miRNA进化方面的系统报道。文章从miRNA的起源以及相应的几种假说、miRNA的产生和消亡、miRNA的功能进化等几方面来分析和综述植物miRNA进化的研究进展。     

A new perspective of human origin and dispersals derived from the microevolution of teeth

Recent genetic studies have heightened the expectation that the origin of modern humans will be defined, but one clear vision has yet to be developed. The study of teeth has historically been an informative means to help define human dispersals. Quantitative tooth data is presented encompassing worldwide human populations. A null hypothesis phylogeny developed from the multivariate analysis of the microevolution of the dental phenotype was interpreted to be broadly in accord with the dominant interpretation of genetic, archaeological, and other dental data by showing that the first division in the dispersion of extant humanity was within sub-Sahara Africans; i.e., San, and Western Africans and Bantu. This "out-of-Africa" interpretation of the graphical results suggests that the first modern human African emigrants not to go extinct were Southeast Asian Negritos. All Eurasians then emerged and expanded through a series of extinct antecedent populations branching from the short lineage extending from Negritos to Australian aborigines. Caucasoids were the first group to fission from this stock. Under this hypothesis, the next to have emerged were antecedent Southeast Asians, from which present Southeast Asians and then antecedent east Central Asians then diverged. Independently, people from the region of Mongolia and all Native Americans arose as daughter populations from antecedent east Central Asians. The broad outline of humanity studied here cannot disprove the equally explanatory protean multiregional hypotheses, but with the inclusion of hominids and further modern human populations either parts of the multiregional hypothesis or the outlined more linear evolutionary scenario likely can be refuted.     

Retroposons in modern human genome evolution

The ascertainment of the rates and driving forces of human genome evolution along with the genetic diversity of populations or separate population groups remains a topical problem of fundamental and applied genomics. According to the results of comparative analysis, the most numerous human genome structure peculiarities are connected with the distribution of mobile genetic retroelements—LTR, LINE1, SVA, and Alu repeats. Due to the wide distribution in different genome loci, conversed retropositional activity, and the retroelements’ regulatory potential, let us regard them as one of the significant evolutionary driving forces and the source of human genome variability. In the current review, we summarize published data and recent results of our research aimed at the analysis of the evolutionary impact of the young retroelements group on the function and variability of the human genome. We examine modern approaches of the polygenomic identification of polymorphic retroelements inserts. Using an original Internet resource, we analyze special features of the genomic polymorphic inserts of AluY repeats. We thoroughly characterize the strategy of large-scale functional analysis of polymorphic retroelement inserts. The presented results confirm the hypothesis of the roles of retroelements as active cis regulatory elements that are able to modulate surrounding genes.     

African human diversity, origins and migrations

The continent of Africa is thought to be the site of origin of all modern humans and is the more recent origin of millions of African Americans. Although Africa has the highest levels of human genetic diversity both within and between populations, it is under-represented in studies of human genetics. Recent advances have been made in understanding the origins of modern humans within Africa, the rate of adaptations due to positive selection, the routes taken in the first migrations of modern humans out of Africa, and the degree of admixture with archaic populations. Africa is also in dire need of effective medical interventions, and studies of genetic variation in Africans will shed light on the genetic basis of diseases and resistance to infectious diseases. Thus, we have tremendous potential to learn about human variation and evolutionary history and to positively impact human health care from studies of genetic diversity in Africa.     

Understanding variation in human fertility: what can we learn from evolutionary demography?

Decades of research on human fertility has presented a clear picture of how fertility varies, including its dramatic decline over the last two centuries in most parts of the world. Why fertility varies, both between and within populations, is not nearly so well understood. Fertility is a complex phenomenon, partly physiologically and partly behaviourally determined, thus an interdisciplinary approach is required to understand it. Evolutionary demographers have focused on human fertility since the 1980s. The first wave of evolutionary demographic research made major theoretical and empirical advances, investigating variation in fertility primarily in terms of fitness maximization. Research focused particularly on variation within high-fertility populations and small-scale subsistence societies and also yielded a number of hypotheses for why fitness maximization seems to break down as fertility declines during the demographic transition. A second wave of evolutionary demography research on fertility is now underway, paying much more attention to the cultural and psychological mechanisms underpinning fertility. It is also engaging with the complex, multi-causal nature of fertility variation, and with understanding fertility in complex modern and transitioning societies. Here, we summarize the history of evolutionary demographic work on human fertility, describe the current state of the field, and suggest future directions.     

Search for genetic markers of climatic adaptation in populations of North Eurasia

Genetic diversity of native populations of North Eurasia is investigated using a panel of genetic markers of candidate genes for cold climate adaptation. A high level of within- and between-population variability is detected. Comparative analysis of data on North Eurasian populations combined with data on worldwide populations from the 1000 Genomes and HDGP projects reveals correlations of genetic diversity in candidate genes for cold climate adaptation with key climate parameters, as well as the increase of genetic diversity in markers of this group of genes with the increase of latitude, that is, as modern humans migrated out of Africa. Using the method of searching for extreme empirical values of the coefficient of genetic diversity, signals of directional selection for markers of six genes adaptive to cold (MYOF, LONP2, IFNL4, MKL1, SLC2A12, and CPT1A) are found. The data are discussed in framework of the hypothesis of decanalization of genome–phenome relationships under the pressure of natural selection during human settlement throughout the world.     

Testing hypotheses about tinkering in the fossil record: the case of the human skull

Efforts to test hypotheses about small-scale shifts in development (tinkering) that can only be observed in the fossil record pose many challenges. Here we use the origin of modern human craniofacial form to explore a series of analytical steps with which to propose and test evolutionary developmental hypotheses about the basic modules of evolutionary change. Using factor and geometric morphometric analyses of craniofacial variation in modern humans, fossil hominids, and chimpanzee crania, we identify several key shifts in integration (defined as patterns of covariation that result from interactions between components of a system) among units of the cranium that underlie the unique shape of the modern human cranium. The results indicate that facial retraction in modern humans is largely a product of three derived changes: a relatively longer anterior cranial base, a more flexed cranial base angle, and a relatively shorter upper face. By applying the Atchley-Hall model of morphogenesis, we show that these shifts are most likely the result of changes in epigenetic interactions between the cranial base and both the brain and the face. Changes in the size of the skeletal precursors to these regions may also have played some role. This kind of phenotype-to-genotype approach is a useful and important complement to more standard genotype-to-phenotype approaches, and may help to identify candidate genes involved in the origin of modern human craniofacial form.     

Evolutionary psychiatry: foundations,progress and challenges

Evolutionary biology provides a crucial foundation for medicine and behavioral science that has been missing from psychiatry. Its absence helps to explain slow progress; its advent promises major advances. Instead of offering a new kind of treatment, evolutionary psychiatry provides a scientific foundation useful for all kinds of treatment. It expands the search for causes from mechanistic explanations for disease in some individuals to evolutionary explanations for traits that make all members of a species vulnerable to disease. For instance, capacities for symptoms such as pain, cough, anxiety and low mood are universal because they are useful in certain situations. Failing to recognize the utility of anxiety and low mood is at the root of many problems in psychiatry. Determining if an emotion is normal and if it is useful requires understanding an individual's life situation. Conducting a review of social systems, parallel to the review of systems in the rest of medicine, can help achieve that understanding. Coping with substance abuse is advanced by acknowledging how substances available in modern environments hijack chemically mediated learning mechanisms. Understanding why eating spirals out of control in modern environments is aided by recognizing the motivations for caloric restriction and how it arouses famine protection mechanisms that induce binge eating. Finally, explaining the persistence of alleles that cause serious mental disorders requires evolutionary explanations of why some systems are intrinsically vulnerable to failure. The thrill of finding functions for apparent diseases is evolutionary psychiatry's greatest strength and weakness. Recognizing bad feelings as evolved adaptations corrects psychiatry's pervasive mistake of viewing all symptoms as if they were disease manifestations. However, viewing diseases such as panic disorder, melancholia and schizophrenia as if they are adaptations is an equally serious mistake in evolutionary psychiatry. Progress will come from framing and testing specific hypotheses about why natural selection left us vulnerable to mental disorders. The efforts of many people over many years will be needed before we will know if evolutionary biology can provide a new paradigm for understanding and treating mental disorders.     

Alternative splicing, the gene concept, and evolution

Alternative splicing allows for the production of many gene products from a single coding sequence. I introduce the concept of alternative splicing via some examples. I then discuss some current hypotheses about the explanatory role of alternative splicing, including the claim that splicing is a significant contributor to the difference in complexity between the human genome and proteosome. Hypotheses such as these bring into question our working concepts of the gene. I examine several gene concepts introduced to cope with processes such as alternative splicing. Next I introduce some hypotheses about the evolution of mechanisms alternative splicing in higher organisms. I conclude that attention to alternative splicing reveals that we adopt an attitude that developmental theorizing must inform evolutionary theorizing and vice versa.     

Opisthobranchia (Mollusca, Gastropoda) – more than just slimy slugs. Shell reduction and its implications on defence and foraging

Genetic studies have typically inferred the effects of human impact by documenting patterns of genetic differentiation and levels of genetic diversity among potentially isolated populations using selective neutral markers such as mitochondrial control region sequences, microsatellites or single nucleotide polymorphism (SNPs). However, evolutionary relevant and adaptive processes within and between populations can only be reflected by coding genes. In vertebrates, growing evidence suggests that genetic diversity is particularly important at the level of the major histocompatibility complex (MHC). MHC variants influence many important biological traits, including immune recognition, susceptibility to infectious and autoimmune diseases, individual odours, mating preferences, kin recognition, cooperation and pregnancy outcome. These diverse functions and characteristics place genes of the MHC among the best candidates for studies of mechanisms and significance of molecular adaptation in vertebrates. MHC variability is believed to be maintained by pathogen-driven selection, mediated either through heterozygote advantage or frequency-dependent selection. Up to now, most of our knowledge has derived from studies in humans or from model organisms under experimental, laboratory conditions. Empirical support for selective mechanisms in free-ranging animal populations in their natural environment is rare. In this review, I first introduce general information about the structure and function of MHC genes, as well as current hypotheses and concepts concerning the role of selection in the maintenance of MHC polymorphism. The evolutionary forces acting on the genetic diversity in coding and non-coding markers are compared. Then, I summarise empirical support for the functional importance of MHC variability in parasite resistance with emphasis on the evidence derived from free-ranging animal populations investigated in their natural habitat. Finally, I discuss the importance of adaptive genetic variability with respect to human impact and conservation, and implications for future studies.     

Evolution of sex: role of deleterious mutation and mobile elements

Prevalence of sexual reproduction is still enigma. The main character of sex is alleles mixing that could be advantageous either in unstable environment (in this case sex provides high temp of evolution) or in unstable genotype (in this case sex provides purge of genome from deleterious mutations). As long as not all species inhabit highly changeable environments, variation of genotypes is more important factor. As the majority of new mutations is deleterious, effective mechanism of genome purging is needed. Maintenance of "purging mechanism" may be a single role of sex. Two promising mutational hypotheses--clade selection (Muller's ratchet and Nunney's hypothesis) and mutational deterministic hypothesis of Kondrashov claim that more effective elimination of slightly-deleterious mutations provides main advantage to sexual population in comparison with asexual. Despite prima facie similarity, these hypotheses differ in mechanisms, work at different temporal scales and have different consequences. Kondrashov's hypothesis reveals short-term advantage of sexual reproduction, and thus, based on the individual selection. Clade selection displays long-term advantage of sexual reproduction that could be realized only by group selection. The role of mobile elements in evolution of sexual reproduction is also discussed. Firstly, mobile elements ("sexual molecular parasites") can complicate the problem: having been domesticated in asexual genomes and remaining active in sexual genomes they lead to higher mutational rate in sexual organisms and so violate assumption critical for both mutational hypotheses of "other things being equal". Secondly, mobile elements could be leader factor of origin of sex (hypothesis proposed by Hickey). Because theory of group selection could explain maintenance of sex, but not its origin, mobile elements could induce the origin of sex but were not able to maintain it, so the next scenario of evolution of sex is proposed: mobile elements induced origin of sex, which was established later by group selection because provided long term benefit (Muller's ratchet and Nunney's hypothesis). So, on all stages of evolution, sex was not advantageous for the organism per se.     

Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data.

To test hypotheses about the origin of modern humans, we analyzed mtDNA sequences, 30 nuclear restriction-site polymorphisms (RSPs), and 30 tetranucleotide short tandem repeat (STR) polymorphisms in 243 Africans, Asians, and Europeans. An evolutionary tree based on mtDNA displays deep African branches, indicating greater genetic diversity for African populations. This finding, which is consistent with previous mtDNA analyses, has been interpreted as evidence for an African origin of modern humans. Both sets of nuclear polymorphisms, as well as a third set of trinucleotide polymorphisms, are highly consistent with one another but fail to show deep branches for African populations. These results, which represent the first direct comparison of mtDNA and nuclear genetic data in major continental populations, undermine the genetic evidence for an African origin of modern humans.     

The zebrafish genome in context: ohnologs gone missing

Some zebrafish genes appear to lack an ortholog in the human genome and researchers often call them "novel" genes. The origin of many so-called "novel" genes becomes apparent when considered in the context of genome duplication events that occurred during evolution of the phylum Chordata, including two rounds at about the origin of the subphylum Vertebrata (R1 and R2) and one round before the teleost radiation (R3). Ohnologs are paralogs stemming from such genome duplication events, and some zebrafish genes said to be "novel" are more appropriately interpreted as "ohnologs gone missing", cases in which ohnologs are preserved differentially in different evolutionary lineages. Here we consider ohnologs present in the zebrafish genome but absent from the human genome. Reasonable hypotheses are that lineage-specific loss of ohnologs can play a role in establishing lineage divergence and in the origin of developmental innovations. How does the evolution of ohnologs differ from the evolution of gene duplicates arising from other mechanisms, such as tandem duplication or retrotransposition? To what extent do different major vertebrate lineages or different teleost lineages differ in ohnolog content? What roles do differences in ohnolog content play in the origin of developmental mechanisms that differ among lineages? This review explores these questions.     

Comparaison de l'expression de certains caractères crâniens sur les hominidés chinois du Pléistocène récent et de l'Holocène (grotte supérieure de Zhoukoudian, sites de Longxian et de Yanqing)

The human remains recovered from “Grotte supérieure de Zhoukoudian” are the best-preserved Late Pleistocene human fossils in East Asia. For decades, as the representative of the Late Pleistocene human in East Asia, the Upper Cave skulls have been playing important role in the research of origins of modern Mongoloids and American Indians. With the advance of the origin and evolution of modern humans, more attention has been paid to the details and the mechanisms for the late Pleistocene human evolution and the formation of modern human populations. Both the origin and diversification of modern humans have been stressed. Some studies further trigger the debaters on the Upper Cave Man concerning its evolutionary level and its role in the formation of modern human populations in East Asia. To further explore these problems, we examined and compared 12 non-metric features on the 3 Late Pleistocene Upper Cave skulls and 162 Holocene individuals earthed from two archaeological sites of North China (Longxian and Yanqing). Our results indicate that 8 on the 12 features have different expression patterns between Upper Cave Man and recent Chinese leading the authors to believe that more primitive expressions appeared on the Upper Cave Man than on recent Chinese populations. Based on these findings, some problems on the intragroup variation in Late Pleistocene and Holocene populations are discussed.     

Life History theory hypotheses on child growth: Potential implications for short and long‐term child growth,development and health

Life history theory integrates ecological, physiological, and molecular layers within an evolutionary framework to understand organisms’ strategies to optimize survival and reproduction. Two life history hypotheses and their implications for child growth, development, and health (illustrated in the South African context) are reviewed here. One hypothesis suggests that there is an energy trade‐off between linear growth and brain growth. Undernutrition in infancy and childhood may trigger adaptive physiological mechanisms prioritizing the brain at the expense of body growth. Another hypothesis is that the period from conception to infancy is a critical window of developmental plasticity of linear growth, the duration of which may vary between and within populations. The transition from infancy to childhood may mark the end of a critical window of opportunity for improving child growth. Both hypotheses emphasize the developmental plasticity of linear growth and the potential determinants of growth variability (including the role of parent–offspring conflict in maternal resources allocation). Implications of these hypotheses in populations with high burdens of undernutrition and infections are discussed. In South Africa, HIV/AIDS during pregnancy (associated with adverse birth outcomes, short duration of breastfeeding, and social consequences) may lead to a shortened window of developmental plasticity of growth. Furthermore, undernutrition and infectious diseases in children living in South Africa, a country undergoing a rapid nutrition transition, may have adverse consequences on individuals’ cognitive abilities and risks of cardio‐metabolic diseases. Studies are needed to identify physiological mechanisms underlying energy allocation between biological functions and their potential impacts on health.     

Multiregional, not multiple origins

Multiregional evolution is a model to account for the pattern of human evolution in the Pleistocene. The underlying hypothesis is that a worldwide network of genic exchanges, between evolving human populations that continually divide and reticulate, provides a frame of population interconnections that allows both species-wide evolutionary change and local distinctions and differentiation. "Multiregional" does not mean independent multiple origins, ancient divergence of modern populations, simultaneous appearance of adaptive characters in different regions, or parallel evolution. A valid understanding of multiregional evolution would go a long way toward reducing the modern human origins controversy.     

Sex and clonality in the little fire ant

Reproduction systems are controlling the creation of new genetic variants as well as how natural selection can operate on these variants. Therefore, they had historically been one of the main foci of evolutionary biology studies. The little fire ant, Wasmannia auropunctata, has been found to display an extraordinary reproduction system, in which both males and female queens are produced clonally. So far, native sexual populations of W. auropunctata have not been identified. Our goals were to identify such sexual populations and investigate the origins of female parthenogenesis and male clonality. Using mitochondrial DNA and microsatellite markers in 17 native populations, we found that traditional sexual populations occurred in W. auropunctata and are likely the recent source of neighboring clonal populations. Queen parthenogenesis has probably evolved several times through mutational events. Male clonality is tightly linked to queen parthenogenesis and thus appears to be female controlled. Its origin could be accounted for by 2 mutually exclusive hypotheses: either by the expected coevolution of the 2 sexes (i.e., a variant of the maternal genome elimination hypothesis) or by a shared mechanistic origin (i.e., by the production of anucleate ovules by parthenogenetic queens). Our results also show that W. auropunctata males and females do not form separate evolutionary units and are unlikely to be engaged in an all-out battle of sexes. This work opens up new perspectives for studies on the adaptive significance and evolutionary stability of mixed sexual and clonal reproduction systems in living organisms.     

山顶洞人与现代华北人头骨非测量性特征比较及中国更新世晚期人类演化的一些问题

山顶洞人化石是迄今在东亚地区发现的数量最为丰富、保存状态最为完好的更新世晚期人类化石。多年来,山顶洞人作为东亚地区更新世晚期人类的代表,在研究东亚地区现代蒙古人种及美洲印第安人起源方面发挥着重要作用。随着对现代人起源与演化研究的深入,学术界对更新世晚期人类演化及现代人群形成过程的许多细节及演化机制予以了越来越多的注意,提出了现代人群出现时间及现代人群分化时间的概念。一些研究对山顶洞人的演化程度及其在东亚地区现代人群形成上的作用也提出了不同看法。为了深入探讨这些问题,本文对12项颅骨非测量特征在山顶洞人与现代中国人的表现情况进行了对比研究。发现有8项特征在山顶洞人与现代中国人之间具有不同的表现,作者认为山顶洞人在颅骨特征表现上较现代中国人具有更多的原始性。在此基础上,作者就更新世晚期人群内部变异、现代人群特征标准等问题进行了讨论。