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© 2015 Taylor & Francis. The complete mitochondrial genome was sequenced in two individuals of white char Salvelinus albus. The genome sequences are 16 653 bp in size, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence detected between the genome of S. albus and the GenBank complete mitochondrial genomes of the Northern Dolly Varden char S. malma (KJ746618) and the Arctic char S. alpinus (AF154851) may likely be due to recent divergence of the species and/or historical hybridization and interspecific replacement of mtDNA.

I will, first, outline what we currently know about the last 4 million years of human evolutionary history, from bipedal but small-brained Australopithecus to modern Homo sapiens, our species, through the prolific toolmaker Homo habilis and the continent wanderer Homo erectus. I shall then identify anatomical traits that distinguish us from other animals and point out our two kinds of heredity, the biological and the cultural. Biological inheritance is based on the transmission of genetic information, in humans very much the same as in other sexually reproducing organisms. But cultural inheritance is distinctively human, based on transmission of information by a teaching and learning process that is in principle independent of biological parentage. Cultural inheritance makes possible the cumulative transmission of experience from generation to generation. Cultural heredity is a swifter and more effective (because it can be designed) mode of adaptation to the environment than the biological mode. The advent of cultural heredity ushered in cultural evolution, which transcends biological evolution. I will, finally, explore ethical behavior as a model case of a distinctive human trait, and seek to ascertain the causal connections between human ethics and human biology. My conclusions are that (1) moral reasoning—that is, the proclivity to make ethical judgments by evaluating actions as either good or evil—is rooted in our biological nature; it is a necessary outcome of our exalted intelligence, but (2) the moral codes that guide our decisions as to which actions are good and which ones are evil are products of culture, including social and religious traditions. This second conclusion contradicts those evolutionists and sociobiologists who claim that the morally good is simply that which is promoted by the process of biological evolution.

We have analyzed DNA sequences from world-wide geographic strains of Plasmodium falciparum and found a complete absence of synonymous DNA polymorphism at 10 gene loci. We hypothesize that all extant world populations of the parasite have recently derived (within several thousand years) from a single ancestral strain. The upper limit of the 95% confidence interval for the time when this most recent common ancestor lived is between 24,500 and 57,500 years ago (depending on different estimates of the nucleotide substitution rate); the actual time is likely to be much more recent. The recent origin of the P. falciparum populations could have resulted from either a demographic sweep ( P. falciparum has only recently spread throughout the world from a small geographically confined population) or a selective sweep (one strain favored by natural selection has recently replaced all others). The selective sweep hypothesis requires that populations of P. falciparum be effectively clonal, despite the obligate sexual stage of the parasite life cycle. A demographic sweep that started several thousand years ago is consistent with worldwide climatic changes ensuing the last glaciation, increased anthropophilia of the mosquito vectors, and the spread of agriculture. P. falciparum may have rapidly spread from its African tropical origins to the tropical and subtropical regions of the world only within the last 6,000 years. The recent origin of the world-wide P. falciparum populations may account for its virulence, as the most malignant of human malarial parasites.

We have analyzed the phylogenetic distribution of introns in the gene coding for xanthine dehydrogenase in 37 species, including 31 dipterans sequenced by us. We have discovered three narrowly distributed novel introns, one in the medfly Ceratitis capitata , the second in the willistoni and saltans groups of Drosophila , and the third in two sibling species of the willistoni group. The phylogenetic distribution of these introns favors the “introns-late” theory of the origin of genes. Analysis of the nucleotide sequences indicates that all three introns have arisen by duplication of a preexisting intron, which is pervasive in Drosophila and other dipterans (and has a homologous position as an intron found in humans and other diverse organisms).

The time of origin of the animal phyla is controversial. Abundant fossils from the major animal phyla are found in the Cambrian, starting 544 million years ago. Many paleontologists hold that these phyla originated in the late Neoproterozoic, during the 160 million years preceding the Cambrian fossil explosion. We have analyzed 18 protein-coding gene loci and estimated that protostomes (arthropods, annelids, and mollusks) diverged from deuterostomes (echinoderms and chordates) about 670 million years ago, and chordates from echinoderms about 600 million years ago. Both estimates are consistent with paleontological estimates. A published analysis of seven gene loci that concludes that the corresponding divergence times are 1,200 and 1,000 million years ago is shown to be flawed because it extrapolates from slow-evolving vertebrate rates to faster-evolving invertebrate rates, as well as in other ways.

The model of predominant clonal evolution (PCE) proposed for micropathogens does not state that genetic exchange is totally absent, but rather, that it is too rare to break the prevalent PCE pattern. However, the actual impact of this "residual" genetic exchange should be evaluated. Multilocus Sequence Typing (MLST) is an excellent tool to explore the problem. Here, we compared online available MLST datasets for seven eukaryotic microbial pathogens: Trypanosoma cruzi, the Fusarium solani complex, Aspergillus fumigatus, Blastocystis subtype 3, the Leishmania donovani complex, Candida albicans and Candida glabrata. We first analyzed phylogenetic relationships among genotypes within each dataset. Then, we examined different measures of branch support and incongruence among loci as signs of genetic structure and levels of past recombination. The analyses allow us to identify three types of genetic structure. The first was characterized by trees with well-supported branches and low levels of incongruence suggesting well-structured populations and PCE. This was the case for the T. cruzi and F. solani datasets. The second genetic structure, represented by Blastocystis spp., A. fumigatus and the L. donovani complex datasets, showed trees with weakly-supported branches but low levels of incongruence among loci, whereby genetic structuration was not clearly defined by MLST. Finally, trees showing weakly-supported branches and high levels of incongruence among loci were observed for Candida species, suggesting that genetic exchange has a higher evolutionary impact in these mainly clonal yeast species. Furthermore, simulations showed that MLST may fail to show right clustering in population datasets even in the absence of genetic exchange. In conclusion, these results make it possible to infer variable impacts of genetic exchange in populations of predominantly clonal micro-pathogens. Moreover, our results reveal different problems of MLST to determine the genetic structure in these organisms that should be considered. Fil: Tomasini, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina Fil: Lauthier, Juan José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina Fil: Ayala, Francisco Jose. University of California Irvine. Department of Ecology and Evolutionary Biology ; Estados Unidos Fil: Tibayrenc, Michel. Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle; Francia Fil: Diosque, Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Salta. Instituto de Patología Experimental; Argentina

Spectral entropy and GC content analyses reveal comprehensive structural features of DNA sequences. To illustrate the significance of these features, we analyze the β-esterase gene cluster, including the Est-6 gene and the ψEst-6 putative pseudogene, in seven species of the Drosophila melanogaster subgroup. The spectral entropies show distinctly lower structural ordering for ψEst-6 than for Est-6 in all species studied. However, entropy accumulation is not a completely random process for either gene and it shows to be nucleotide dependent. Furthermore, GC content in synonymous positions is uniformly higher in Est-6 than in ψEst-6, in agreement with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of ψEst-6 and Est-6 after the duplication event. The data obtained show the relevance and significance of entropy and GC content analyses for pseudogene identification and for the comparative study of gene-pseudogene evolution.

We have analyzed the comportment in in vitro culture of 2 different genotypes of Trypanosoma cruzi, the agent of Chagas disease, pertaining to 2 major genetic subdivisions (near-clades) of this parasite. One of the stocks was a fast-growing one, highly virulent in mice, while the other one was slow- growing, mildly virulent in mice. The working hypothesis was that mixtures of genotypes interact, a pattern that has been observed by us in empirical experimental studies. Genotype mixtures were followed every 7 days and characterized by the DIGE technology of proteomic analysis. Proteic spots of interest were characterized by the SAMESPOT software. Patterns were compared to those of pure genotypes that were also evaluated every 7 days. One hundred and three spots exhibited changes in time by comparison with T = 0. The major part of these spots (58%) exhibited an under-expression pattern by comparison with the pure genotypes. 32% of the spots wereover-expressed; 10% of spots were not different from those of pure genotypes. Interestingly, interaction started a few minutes after the mixtures were performed. We have retained 43 different proteins that clearly exhibited either under- or over-expression. Proteins showing interaction were characterized by mass spectrometry (MALDI-TOF). Close to 50% of them were either tubulins or heat shock proteins. This study confirms that mixed genotypes of T. cruzi interact at the molecular level. This is of great interest because mixtures of genotypes are very frequent in Chagas natural cycles, both in insect vectors and in mammalian hosts, and may play an important role in the transmission and severity of Chagas disease. The methodology proposed here is potentially applicable to any micropathogen, including fungi, bacteria and viruses. It should be of great interest in the case of bacteria, for which the epidemiological and clinical consequences of mixed infections could be underestimated.

Until the 1990s, Plasmodium and Toxoplasma were widely considered to be potentially panmictic species, because they both undergo a meiotic sexual cycle in their definitive hosts. We have proposed that both parasites are able of clonal (nonrecombining) propagation, at least in some cycles. Toxoplasma was soon shown to be a paradigmatic case of clonal population structure in North American and in European cycles. But the proposal provoked an outcry in the case of Plasmodium and still appears as doubtful to many scientists. However, the existence of Plasmodium nonrecombining lines has been fully confirmed, although the origin of these lines is debatable. We discuss the current state of knowledge concerning the population structure of both parasites in the light of the recent developments of pathogen clonal evolution proposed by us and of new hypotheses presented here.

Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease, to identify major lineages and to unravel their past history of divergence and possible recombination events. At the scale of T. cruzi subspecific diversity, graph theory-based networks applied to 22 isoenzyme loci (262 distinct Multi-Locus-Enzyme-Electrophoresis -MLEE) and 19 microsatellite loci (66 Multi-Locus-Genotypes -MLG) fully confirms the high clustering of genotypes into major lineages or "near-clades". The release of the dichotomic constraint associated with phylogenetic reconstruction usually applied to Multilocus data allows identifying putative hybrids and their parental lineages. Reticulate topology suggests a slightly different history for some of the main "near-clades", and a possibly more complex origin for the putative hybrids than hitherto proposed. Finally the sub-network of the near-clade T. cruzi I (28 MLG) shows a clustering subdivision into three differentiated lesser near-clades ("Russian doll pattern"), which confirms the hypothesis recently proposed by other investigators. The present study broadens and clarifies the hypotheses previously obtained from classical markers on the same sets of data, which demonstrates the added value of this approach. This underlines the potential of graph theory-based network analysis for describing the nature and relationships of major pathogens, thereby opening stimulating prospects to unravel the organization, dynamics and history of major micropathogen lineages. © 2014 Arnaud-Haond et al.

Theodosius Dobzhansky (1900–1975) was a key author of the Synthetic Theory of Evolution, also known as the Modern Synthesis of Evolutionary Theory, which embodies a complex array of biological knowledge centered around Darwin’s theory of evolution by natural selection couched in genetic terms. The epithet “synthetic” primarily alludes to the artful combination of Darwin’s natural selection with Mendelian genetics, but also to the incorporation of relevant knowledge from biological disciplines. In the 1920s and 1930s several theorists had developed mathematical accounts of natural selection as a genetic process. Dobzhansky’s Genetics and the Origin of Species , published in 1937 (1), refashioned their formulations in language that biologists could understand, dressed the equations with natural history and experimental population genetics, and extended the synthesis to speciation and other cardinal problems omitted by the mathematicians. The current Synthetic Theory has grown around that original synthesis. It is not just one single hypothesis (or theory) with its corroborating evidence, but a multidisciplinary body of knowledge bearing on biological evolution, an amalgam of well-established theories and working hypotheses, together with the observations and experiments that support accepted hypotheses (and falsify rejected ones), which jointly seek to explain the evolutionary process and its outcomes. These hypotheses, observations, and experiments often originate in disciplines such as genetics, embryology, zoology, botany, paleontology, and molecular biology. Currently, the “synthetic” epithet is often omitted and the compilation of relevant knowledge is simply known as the Theory of Evolution. This is still expanding, just like one of those “holding” business corporations that have grown around an original enterprise, but continue incorporating new profitable enterprises and discarding unprofitable ones. Darwin summarized the theory of evolution by natural selection in the Origin of Species (2) as follows: “As many more individuals are produced than can possibly survive, there must in every case …

The Drosophila obscura group consists of several dozen Nearctic and Palearctic species, with a phylogeny that remains largely unresolved in spite of numerous morphological, cytogenetic, and molecular investigations. We have partially sequenced two genes, Gpdh (about 1000 bp) and Sod (about 700 bp) in 12-13 species and 1 subspecies in order to settle the issues. Difficulties in resolving the phylogeny emanate from the rapid sequence of successive radiations. Nevertheless, the following conclusions are warranted: (1) The Palearctic species include two monophyletic subgroups, subobscura (which may be the most ancient clade of the whole group) and obscura, plus two other species with unresolved phylogenetic positions, D. bifasciata and D. subsilvestris; (2) the Nearctic species form a monophyletic group consisting of two monophyletic sister clades, the affinis subgroup and the pseudoobscura subgroup. The Palearctic radiation may have resulted from adaptation to expanding temperate forests in the Old World. A second radiation occurred during the colonization of the deciduous forests of the New World by the descendants of a single lineage that soon split into the affinis and pseudoobscura subgroups.

Trypanosoma brucei, a pathogen of human and domestic animals, is an early evolved parasitic protozoan with a complex life cycle. Most genes of this parasite are post-transcriptionally regulated. However, the mechanisms and the molecules involved remain largely unknown. We have deep-sequenced the small RNAs of two life stages of this parasite—the bloodstream form and the procyclic form. Our results show that the small RNAs of T. brucei could derive from multiple sources, including NATs (natural antisense transcripts), tRNAs, and rRNAs. Most of these small RNAs in the two stages were found to share uniform characteristics. However, our results demonstrate that their variety and expression show significant differences between different stages, indicating possible functional differentiation. Dicer-knockdown evidence further proved that some of the small interfering RNAs (siRNAs) could regulate the expression of genes. Based on the genome-wide analysis of the small RNAs in the two stages of T. brucei, our results not only provide evidence to study their differentiation but also shed light on questions regarding the origins and evolution of small RNA-based mechanisms in early eukaryotes.

The clonal theory of parasitic protozoa has been recently challenged by researchers stating that recombination in Kinetoplastida is much more frequent than previously believed, or that selfing and homogamy should be distinguished from ‘strict’ clonality. These researchers and many others show that the concept of clonality proposed by us is not correctly understood. A recapitulation of the clonal theory will thus be addressed herein. Comparisons with various other pathogens evidence general features among them and enhance our understanding of Trypanosoma and Leishmania population genetics. The relevance is considerable not only for our knowledge of the basic biology of these organisms but also for applied research: molecular epidemiology (strain-typing), clinical research, vaccine and drug design, and experimental evolution.

We have amplified and sequenced the gene encoding Esterase-P (Est-P) in 10 strains of Drosophila melanogaster. Three premature termination codons occur in the coding region of the gene in two strains. This observation, together with other indirect evidence, leads us to propose that Est-P may he a pseudogene in D. melanogaster. Est-P would he a “cryptic” pseudogene, in the sense that it retains intact the coding sequence (without stop codons and other alterations usually observed in pseudogenes) in most D. melanogaster strains. We conjecture that the β-esterase cluster may consist in other Drosophila species of functional and nonfunctional genes. We also conjecture that the rarity of detected pseudogenes in Drosophila may he due to the difficulty of discovering them, because most of them are cryptic.

We propose a simple algorithm for estimating the number of nucleotide differences between a pair of RNA or DNA sequences through comparison of their RNAse A mismatch cleavage patterns. In the RNAse A mismatch cleavage technique two or more sample sequences are hybridized to the same RNA probe, the hybrids are partially digested with RNAse A, and the digestion products are compared on an electrophoretic gel. Here we provide an algorithm for converting the numbers of unique and matching electrophoretic bands into an estimate of the number of nucleotide differences between the sequences. Computer simulation indicates that the proposed method yields a robust estimate of the genetic distance despite stochastic errors and occasional violation of certain assumptions. Our study suggests that the method performs best when the distance between the sequences is

Human evolution exhibits repeated speciations and conspicuous morphological change: from Australopithecus to Homo habilis, H. erectus, and H. sapiens; and from their hominoid ancestor to orangutans, gorillas, chimpanzees, and humans. Theories of founder-event speciation propose that speciation often occurs as a consequence of population bottlenecks, down to one or very few individual pairs. Proponents of punctuated equilibrium claim in addition that founder-event speciation results in rapid morphological change. The major histocompatibility complex (MHC) consists of several very polymorphic gene loci. The genealogy of 19 human alleles of the DQB1 locus coalesces more than 30 million years ago, before the divergence of apes and Old World monkeys. Many human alleles are more closely related to pongid and cercopithecoid alleles than to other human alleles. Using the theory of gene coalescence, we estimate that these polymorphisms require human populations of the order of N = 100,000 individuals for the last several million years. This conclusion is confirmed by computer simulations showing the rate of decay of the polymorphisms over time. Computer simulations indicate, in addition, that in human evolution no bottlenecks have occurred with fewer than several thousand individuals. We evaluate studies of mtDNA, Y-chromosome, and microsatellite autosomal polymorphisms and conclude that they are consistent with the MHC result that no narrow population bottlenecks have occurred in human evolution. The available molecular information favors a recent African origin of modern humans, who spread out of Africa approximately 100,000 to 200,000 years ago.

Die Biologen sind sich einig, dass das Leben auf unserem Planeten spontan durch naturliche Vorgange entstanden ist, und zwar aus denselben chemischen Elementen, aus denen die Organismen noch heute bestehen – darunter Kohlenstoff, Stickstoff, Sauerstoff und Wasserstoff. Heist das, dass wir wissen, wie das Leben begonnen hat? Nicht ganz. Zwar gibt es einige uberzeugende Vorstellungen und Experimente zur Entstehung des Lebens, aber es gibt noch keinen Konsens. Wir konnen allerdings mit groser Sicherheit davon ausgehen, dass alle Geschopfe auf der Erde von einer einzigen gemeinsamen Urlebensform abstammen.

Der Stammbaum des Lebens (universal tree of life) umfasst alle Lebewesen von ihrem gemeinsamen Urahnen bis heute. Die taxonomischen Gruppen bilden die Aste des Baums. Dieser Baum hat drei Hauptaste oder Domanen: Eukaryoten, Bakterien und Archaeen; die beiden letztgenannten sind mikroskopisch kleine Prokaryoten. Die meisten eukaryotischen Organismen sind ebenfalls winzig kleine Einzeller; den Rest bilden die uns vertrauten vielzelligen Tiere, Pflanzen und Pilze. Alle Organismen sind miteinander verwandt; sie stammen von einem gemeinsamen Urahnen ab: LUCA, dem last universal common ancestor, zu Deutsch: letzter allgemeiner gemeinsamer Vorfahr.

Im Jahr 1871, zwolf Jahre nach Uber die Entstehung der Arten, erschien Die Abstammung des Menschen, das Werk, in dem Darwin seine Theorie der Evolution durch naturliche Selektion auf den Menschen ausdehnte. Fossilien von Ubergangsformen zwischen Menschenaffen und Menschen waren noch nicht entdeckt worden, und Darwins Kritiker wurden nicht mude, auf dieses fehlende Bindeglied – das Missing Link – hinzuweisen. Das Bindeglied fehlt nicht langer. Seit Darwins Zeiten wurden Tausende von Uberresten solcher Ubergangsformen, der sogenannten Hominiden, gefunden, und das Tempo der Entdeckungen zieht immer noch an.

The theory of biological evolution is the central organizing principle of modern biology. In 1973, the eminent evolutionist Theodosius Dobzhansky famously asserted that “Nothing in biology makes sense except in the light of evolution.” Evolution provides a scientific explanation for why there are so many different kinds of organisms on Earth and gives an account of their similarities and differences (morphological, physiological, and genetic). Science has demonstrated again and again, beyond reasonable doubt, that living organisms evolve and diversify over time, and that their features have come about by natural selection, a process that accounts for their design. Yet, there are many people of faith in the United States and elsewhere who think that science, particularly the theory of evolution, is contrary to the teachings of the Bible and to religious beliefs, such as creation by God. Well before the formulation of the theory of evolution, religious authors over the centuries used the “argument-from-design” to demonstrate rationally, without reference to faith or divine revelation, the existence of God, as the author of the design of organisms. The argument from design has two parts. In one familiar form it asserts, first, that organisms evince to have been designed; second, that only God could account for the design. The argument from design was advanced, in a variety of forms, in Classical Greece and early Christianity. Its most extensive formulation is due to William Paley in his Natural Theology (Natural theology, or evidences of the existence and attributes of the deity collected from the appearances of nature. American Tract Society, New York, 1802). The eye—as well as all sorts of organs, organisms, and their interactions—manifests to be the outcome of design and not of chance, thus it shows to have been created by God. In the 1990s, the design argument was revived in the United States by several authors. The flagellum used by bacteria for swimming and the immune system of mammals, as well as some improbability calculations, were advanced as evidence of “intelligent design,” on the grounds that chance processes could not account for the phenomena to be explained. In The Origin of Species, Darwin (On the origin of species by means of natural selection. John Murray, London, 1859) advanced a scientific explanation of the design of organisms. The adaptations of organisms are outcomes not of chance, but of a process that, over time, causes the gradual accumulation of features beneficial to organisms, whenever these features increase the organisms’ chances of surviving and reproducing. There is design in the living world: eyes are designed for seeing, wings for flying, and kidneys for regulating the composition of the blood. The design of organisms comes about not by intelligent design, but by a natural process, which is creative through the interaction of chance and necessity. Organisms are pervaded by imperfections, dysfunctions, cruelties, and even sadism. The theory of evolution accounts for these mishaps by natural selection, as outcomes of natural processes, so that they need not be attributed to God’s explicit design. The theory of evolution perceived by some people of faith as contrary to religion, may thus be acknowledged as their “disguised friend.” The theory of evolution accounts for the design of organisms, but also for the dysfunctions, oddities, cruelty, and sadism that pervade the world of life, so that these deficiencies need not be attributed to specific agency by the Creator, which might implicitly amount to blasphemy. The foregoing considerations are important both for understanding and for accepting evolution as a fact of life, and should be taken into account by science educators and teachers.

Die Ontogenese, also die Entwicklung von der Eizelle zum ausgewachsenen Organismus, und der Zusammenhang zwischen Gehirn und Geist sind zwei der grosen Forschungsthemen der Biologie im 21. Jahrhundert. Bei der Ontogenese geht es um die Frage, wie die eindimensionale genetische Information, die in der DNA einer einzelnen Zelle niedergelegt ist, in ein vierdimensionales Wesen transformiert wird: in ein Individuum, das wachst, heranreift und stirbt. Das Gehirn-Geist-Ratsel besteht aus zwei miteinander verflochtenen Teilfragen: Wie werden die physikochemischen Signale, die unsere Sinnesorgane erreichen, in Wahrnehmungen, Gefuhle, Gedanken, kritische Argumente, asthetische Empfindungen und ethische Werte transformiert? Und wie konstituiert sich aus dieser Vielzahl an Erfahrungen eine einheitliche Realitat: der Geist oder das Selbst?

„Im Anfang schuf Gott Himmel und Erde … Gott sprach: Es werde Licht. Und es wurde Licht. … und Gott nannte das Licht Tag und die Finsternis nannte er Nacht. Es wurde Abend und es wurde Morgen: erster Tag. … Gott schuf also den Menschen als sein Abbild; als Abbild Gottes schuf er ihn. Als Mann und Frau schuf er sie. Gott sah alles an, was er gemacht hatte: Es war sehr gut. Es wurde Abend und es wurde Morgen: der sechste Tag.“9

Plasmodium vivax is considered to be absent from Central and West Africa because of the protective effect of Duffy negativity. However, there are reports of persons returning from these areas infected with this parasite and observations suggesting the existence of transmission. Among the possible explanations for this apparent paradox, the existence of a zoonotic reservoir has been proposed. May great apes be this reservoir? We analyze the mitochondrial and nuclear genetic diversity of P. vivax parasites isolated from great apes in Africa and compare it to parasites isolated from travelers returning from these regions of Africa, as well as to human isolates distributed all over the world. We show that the P. vivax sequences from parasites of great apes form a clade genetically distinct from the parasites circulating in humans. We show that this clade’s parasites can be infectious to humans by describing the case of a traveler returning from the Central African Republic infected with one of them. The relationship between this P. vivax clade in great apes and the human isolates is discussed.

„In diesem Wettkampfe werden Abanderungen, wie gering … sie auch … sein mogen, wenn sie nur fur die Individuen einer Art … einigermasen vorteilhaft sind, zur Erhaltung solcher Individuen beitragen und sich meistens durch Vererbung auf deren Nachkommen ubertragen. … Dieses Prinzip, wonach jede nutzliche, wenn auch nur geringe Abanderung erhalten wird, habe ich ‚naturliche Zuchtwahl’ genannt … Doch ist der von Herbert Spencer oft gebrauchte Ausdruck ‚Uberleben des Passendsten’ (survival of the fittest) zutreffender und zuweilen ebenso bequem.“4

Die genetische Ausstattung eines Menschen kann man klonen, das Individuum hingegen nicht. Ein Individuum ist das Produkt der Wechselwirkungen zwischen seinem Genotyp und seiner Umwelt. Die genetische Ausstattung einer Person wird bei der Befruchtung festgelegt. Sie besteht aus zwei Satzen von Genen, einem vom Vater und einem von der Mutter. Zur Umwelt gehoren alle Erfahrungen, denen dieser Genotyp seit der Empfangnis ausgesetzt war, vom Mutterleib uber die Kindheit, Schule und Familie bis hin zur Gesellschaft.

Menschen sind Tiere, aber Tiere ganz besonderer Art. Zu unseren anatomischen Besonderheiten zahlen der aufrechte Gang und das enorme Gehirn. Noch wichtiger ist unser einzigartiges individuelles und soziales Verhalten. Die biologische Evolution setzt sich im modernen Menschen fort, aber mit dem Aufkommen der Menschheit hat eine kulturelle Evolution eingesetzt, die uns schneller und effektiver an unsere Umwelt anpasst als der biologische Entwicklungsmodus. Zu den Produkten der kulturellen Evolution gehoren Wissenschaft und Technik, soziale und politische Institutionen, Religion und Ethik, Sprache, Literatur und Kunst sowie elektronische Kommunikation.

Arten (species) entstehen durch die allmahlichen Veranderungen, die die naturliche Selektion bewirkt. Die Umwelt der Organismen wandelt sich mit der Zeit und unterscheidet sich von Ort zu Ort. Daher begunstigt die naturliche Selektion je nach Situation unterschiedliche Merkmale. Die Akkumulation der Unterschiede fuhrt schlieslich zur Entstehung von Arten.

Darwins Theorie der Evolution durch naturliche Selektion traf zu seinen Lebzeiten bei seinen Zeitgenossen und auch spater unter anderem deshalb auf Widerstande, weil sie keine taugliche Vererbungstheorie enthielt. Im Jahr 1866 veroffentlichte der Augustinermonch Gregor Mendel die Grundprinzipien einer Vererbungslehre (theory of heredity), die nach wie vor gultig sind. Die genetische Information ist demnach in einzelnen Erbfaktoren, den Genen, enthalten, die paarweise vorliegen, da beide Eltern je ein Exemplar beisteuern.

Wenn ein Nichtwissenschaftler gefragt wird, welche Eigenschaft er fur die menschlichste halt, also fur diejenige, die uns am eindeutigsten von den ubrigen Menschenaffen unterscheidet, wird er hochstwahrscheinlich einen Aspekt des menschlichen Geistes nennen. Es konnte das Gehirn sein, das bei uns etwa viermal so gros ist wie bei den Schimpansen oder Gorillas, oder ein funktionales Merkmal wie Sprache, komplexe soziale Strukturen oder Technik. Oft durfte unsere „uberragende Intelligenz“ erwahnt werden, die aus unserem grosen Gehirn resultiert und mit den anderen funktionellen Merkmalen zusammenhangt.

„Palaontologen haben die Fossilien Abertausender Organismen aus der Erdvergangenheit geborgen und untersucht. Diese Funde zeigen, dass es unter den ausgestorbenen Organismen viele Typen gab, die sich in ihrer Form von allen heutigen Lebewesen unterschieden. Die fossile Uberlieferung belegt auch Abfolgen von Organismen im Laufe der Zeit und Ubergange von einer Form zu einer anderen.“5

„Naturwissenschaftler verwenden den Ausdruck ‚Tatsache’ fur eine wissenschaftliche Erklarung, die so oft uberpruft und bestatigt wurde, dass es keinen uberzeugenden Grund mehr gibt, sie noch einmal zu uberprufen oder nach weiteren Beispielen zu suchen … Da die Belege [fur die Evolution] so stark sind, stellen sich Naturwissenschaftler nicht mehr die Frage, ob eine biologische Evolution stattgefunden hat oder noch stattfindet. Statt- dessen untersuchen sie die Mechanismen der Evolution, die Geschwindigkeit, mit der sie ablaufen kann, und ahnliche Fragestellungen.“2

„Der bestandige Gebrauch der artikulierten Sprache ist jedoch dem Menschen eigentumlich; aber er benutzt wie die niederen Tiere unartikulierte Ausrufe in Verbindung mit Gesten und den Bewegungen seiner Gesichtsmuskeln, um seine Gedanken auszudrucken. Dies gilt besonders fur die einfacheren und lebhafteren Gefuhle, welche mit unserer hoheren Intelligenz nur wenig im Zusammenhang stehen. … Nicht also die blose Fahigkeit der Artikulation ist das unterscheidende Merkmal … Von den Tieren unterscheidet sich der Mensch allein durch seine unendlich grosere Fahigkeit, die verschiedenartigsten Laute und Ideen zu assoziieren, und dies hangt offenbar von der hohen Entwicklung seiner geistigen Fahigkeiten ab.“8

Die Evolution der Organismen steht im Mittelpunkt vieler biologischer Disziplinen wie der Genetik, Molekularbiologie, Biochemie, Neurobiologie, Physiologie und der Okologie und macht das Auftauchen neuer Krankheiten, die Entwicklung von Antibiotika- resistenzen bei Bakterien und weitere Probleme des Gesundheitswesens verstandlich. Die Evolution erklart die okologischen Beziehungen zwischen wilden und domestizierten Pflanzen und Tieren. Das Konzept kommt auch in der Informatik, bei der Entwicklung chemischer Verbindungen und in etlichen weiteren Industrie- zweigen zum Einsatz.

Die molekulare Evolutionsbiologie (molecular evolution) ist jene biologische Disziplin, in der die Evolution mit den Mitteln der Molekularbiologie untersucht wird. Sie kam Mitte des 20. Jahrhunderts auf, nachdem 1953 die Doppelhelixstruktur unseres Erbmolekuls, der DNA, aufgeklart worden war. Die Molekularbiologie liefert die starksten Belege fur die biologische Evolution und ermoglicht uns eine nahezu beliebig detaillierte und genaue Rekonstruktion der Stammesgeschichte der Lebewesen.

Die gemeinsamen Vorfahren von Menschen und Schimpansen lebten noch vor sechs bis sieben Millionen Jahren. Menschen, Menschenaffen und die ubrigen Affen sind allesamt Primaten, aber der Mensch ist ein ganz besonderer Primat. Wir haben den aufrechten Gang, ein groses Gehirn und opponierbare Daumen, die uns die prazise Handhabung von Werkzeugen und anderen Gegenstanden ermoglichen. Und was noch wichtiger ist: Menschen sind sehr intelligent und verfugen uber Kultur, zu der Sprache, hoch entwickelte Techniken und komplexe soziale und politische Institutionen ebenso zahlen wie Ethik und Religion.

It has been proposed that modern humans descended from a single woman, the "mitochondrial Eve" who lived in Africa 100,000 to 200,000 years ago. The human immune system DRB1 genes are extremely polymorphic, with gene lineages that coalesce into an ancestor who lived around 60 million years ago, a time before the divergence of the apes from the Old World monkeys. The theory of gene coalescence suggests that, throughout the last 60 million years, human ancestral populations had an effective size of 100,000 individuals or greater. Molecular evolution data favor the African origin of modern humans, but the weight of the evidence is against a population bottleneck before their emergence. The mitochondrial Eve hypothesis emanates from a confusion between gene genealogies and individual genealogies.

The exon theory of genes proposes that the introns of protein-encoding nuclear genes are remnants of the DNA spacers between ancient minigenes. The discovery of an intron at a predicted position in the triose-phosphate isomerase (EC 5.3.1.1) gene of Culex mosquitoes has been hailed as an evidential pillar of the theory. We have found that that intron is also present in Aedes mosquitoes, which are closely related to Culex, but not in the phylogenetically more distant Anopheles, nor in the fly Calliphora vicina, nor in the moth Spodoptera littoralis. The presence of this intron in Culex and Aedes is parsimoniously explained as the result of an insertion in a recent common ancestor of these two species rather than as the remnant of an ancient intron. The absence of the intron in 19 species of very diverse organisms requires at least 10 independent evolutionary losses in order to be consistent with the exon theory.

We have tested a new genetic marker, RADES Probing (RADES-P), on a standard sample of 19 laboratory-cloned stocks of Trypanosoma cruzi, the agent of Chagas disease. This set of stocks, fully characterized using multilocus enzyme electrophoresis (MLEE) and random amplified polymorphic DNA (RAPD), is representative of this parasite's main genetic subdivisions. RADES-P consists in hybridizing RAPD profiles with probes composed of the products of random amplified differentially expressed sequences (RADES). The profiles thus obtained uncover only expressed coding sequences that are as well present on RAPD gels. Direct visual examination and the banding record show that these RADES-P profiles are different of, and not redundant with, both RAPD and RADES patterns obtained on the same set of stocks with the same primers. Phylogenetic character mapping (PCM) of the RADES-P polymorphism fairly confirms the known population structure and phylogenetic diversity of T. cruzi. This suggests that the impact of clonal evolution on T. cruzi has been predominant enough over the long term to carve the polymorphism of all types of DNA sequences, including polymorphisms of expressed coding sequences, although these sequences are subject to natural selection. © 2013 Elsevier B.V.

We propose that clonal evolution in micropathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure, a definition already widely used for all kinds of pathogens, although not clearly formulated by many scientists and rejected by others. The two main manifestations of clonal evolution are strong linkage disequilibrium (LD) and widespread genetic clustering (“near-clading”). We hypothesize that this pattern is not mainly due to natural selection, but originates chiefly from in-built genetic properties of pathogens, which could be ancestral and could function as alternative allelic systems to recombination genes (“clonality/sexuality machinery”) to escape recombinational load. The clonal framework of species of pathogens should be ascertained before any analysis of biomedical phenotypes (phylogenetic character mapping). In our opinion, this model provides a conceptual framework for the population genetics of any micropathogen.

In On the Origin of Species by Means of Natural Selection (1859), Darwin (1) barely mentioned the brain. Only in The Descent of Man, and Selection in Relation to Sex (2), published in 1871, did Darwin emphasize that the human nervous system, like any other organ system, must have evolved. Even so, Darwin himself wrote little on the brain. Instead, Darwin asked his good friend T. H. Huxley to write a chapter for the second edition of The Descent of Man, and Selection in Relation to Sex that dealt specifically with human brain evolution. In this chapter, Huxley laid to rest Richard Owen’s earlier argument that human brains are outliers among mammalian brains. Instead, Huxley argued that our brains resemble the brains of other apes in all fundamental respects. He even downplayed the greater size of human brains, noting that brain size is quite variable among humans. Importantly, Huxley did not deny that our brains must somehow differ from the brains of other apes, for he could see no other way to explain our unique cognitive capacities, most notably language. However, Huxley postulated that the differences that set our brains apart are not apparent in gross dissections (3⇓⇓⇓–7). ### Box 1. In the light of evolution. In 1973, Dobzhansky (45) penned a short commentary titled “Nothing in biology makes sense except in the light of evolution.” Most scientists agree that evolution provides the unifying framework for interpreting biological phenomena that otherwise can often seem unrelated and perhaps unintelligible. Given the central position of evolutionary thought in biology, it is sadly ironic that evolutionary perspectives outside the sciences have often been neglected, misunderstood, or purposefully misrepresented. Biodiversity—the genetic variety of life—is an exuberant product of the evolutionary past, a vast human-supportive resource (aesthetic, intellectual, and material) of the … [↵][1]1To whom correspondence should be addressed. E-mail: fjayala{at}uci.edu. [1]: #xref-corresp-1-1

The brown alga Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is a highly polymorphic representative of the family Laminariaceae, inhabiting the northwest Pacific region. We have obtained 16S rRNA sequence data in symbiont microorganisms of the typical form (TYP) of S. japonica and its common morphological varieties, known as "longipes" (LON) and "shallow-water" (SHA), which show contrasting bathymetric distribution and sharp morphological, life history traits, and ecological differences. Phylogenetic analysis of the 16S rRNA sequences shows that the microbial communities are significantly different in the three forms studied and consist of mosaic sets of common and form-specific bacterial lineages. The divergence in bacterial composition is substantial between the TYP and LON forms in spite of their high genetic similarity. The symbiont distribution in the S. japonica forms and in three other laminarialean species is not related to the depth or locality of the algae settlements. Combined with our previous results on symbiont associations in sea urchins and taking into account the highly specific character of bacteria-algae associations, we propose that the TYP and LON forms may represent incipient species passing through initial steps of reproductive isolation. We suggest that phenotype differences between genetically similar forms may be caused by host-symbiont interactions that may be a general feature of evolution in algae and other eukaryote organisms. Bacterial symbionts could serve as sensitive markers to distinguish genetically similar algae forms and also as possible growth-promoting inductors to increase algae productivity.

The origin of Plasmodium falciparum in South America is controversial. Some studies suggest a recent introduction during the European colonizations and the transatlantic slave trade. Other evidence—archeological and genetic—suggests a much older origin. We collected and analyzed P. falciparum isolates from different regions of the world, encompassing the distribution range of the parasite, including populations from sub-Saharan Africa, the Middle East, Southeast Asia, and South America. Analyses of microsatellite and SNP polymorphisms show that the populations of P. falciparum in South America are subdivided in two main genetic clusters (northern and southern). Phylogenetic analyses, as well as Approximate Bayesian Computation methods suggest independent introductions of the two clusters from African sources. Our estimates of divergence time between the South American populations and their likely sources favor a likely introduction from Africa during the transatlantic slave trade.