Genetic Variation among Major Human Geographic Groups Supports a Peculiar Evolutionary Trend in PAX9

A total of 172 persons from nine South Amerindian, three African and one Eskimo populations were studied in relation to the Paired box gene 9 (PAX9) exon 3 (138 base pairs) as well as its 5' and 3' flanking intronic segments (232 bp and 220 bp, respectively) and integrated with the information available for the same genetic region from individuals of different geographical origins. Nine mutations were scored in exon 3 and six in its flanking regions; four of them are new South American tribe-specific singletons. Exon3 nucleotide diversity is several orders of magnitude higher than its intronic regions. Additionally, a set of variants in the PAX9 and 101 other genes related with dentition can define at least some dental morphological differences between Sub-Saharan Africans and non-Africans, probably associated with adaptations after the modern human exodus from Africa. Exon 3 of PAX9 could be a good molecular example of how evolvability works.

Testing Evolutionary and Dispersion Scenarios for the Settlement of the New World

Background: Discussion surrounding the settlement of the New World has recently gained momentum with advances in molecular biology, archaeology and bioanthropology. Recent evidence from these diverse fields is found to support different colonization scenarios. The currently available genetic evidence suggests a ""single migration'' model, in which both early and later Native American groups derive from one expansion event into the continent. In contrast, the pronounced anatomical differences between early and late Native American populations have led others to propose more complex scenarios, involving separate colonization events of the New World and a distinct origin for these groups. Methodology/Principal Findings: Using large samples of Early American crania, we: 1) calculated the rate of morphological differentiation between Early and Late American samples under three different time divergence assumptions, and compared our findings to the predicted morphological differentiation under neutral conditions in each case; and 2) further tested three dispersal scenarios for the colonization of the New World by comparing the morphological distances among early and late Amerindians, East Asians, Australo-Melanesians and early modern humans from Asia to geographical distances associated with each dispersion model. Results indicate that the assumption of a last shared common ancestor outside the continent better explains the observed morphological differences between early and late American groups. This result is corroborated by our finding that a model comprising two Asian waves of migration coming through Bering into the Americas fits the cranial anatomical evidence best, especially when the effects of diversifying selection to climate are taken into account. Conclusions: We conclude that the morphological diversity documented through time in the New World is best accounted for by a model postulating two waves of human expansion into the continent originating in East Asia and entering through Beringia.

Singing in the Rain Forest: How a Tropical Bird Song Transfers Information

How information transmission processes between individuals are shaped by natural selection is a key question for the understanding of the evolution of acoustic communication systems. Environmental acoustics predict that signal structure will differ depending on general features of the habitat. Social features, like individual spacing and mating behavior, may also be important for the design of communication. Here we present the first experimental study investigating how a tropical rainforest bird, the white-browed warbler Basileuterus leucoblepharus, extracts various information from a received song: species-specific identity, individual identity and location of the sender. Species-specific information is encoded in a resistant acoustic feature and is thus a public signal helping males to reach a wide audience. Conversely, individual identity is supported by song features susceptible to propagation: this private signal is reserved for neighbors. Finally, the receivers can locate the singers by using propagation-induced song modifications. Thus, this communication system is well matched to the acoustic constraints of the rain forest and to the ecological requirements of the species. Our results emphasize that, in a constraining acoustic environment, the efficiency of a sound communication system results from a coding/decoding process particularly well tuned to the acoustic properties of this environment.

Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies

Background: The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized. Results: We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for similar to 40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance. Conclusion: These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.

Harvest-ironman: heavy armature, and not its defensive secretions, protects a harvestman against a spider

Natural selection has caused prey species to evolve distinct defensive mechanisms. One of such mechanisms was the evolution of noxious or distasteful chemicals, which have appeared independently in a number of vertebrates and invertebrates. In detailed analyses of arthropod behaviour, scent gland secretions have consistently been shown to be responsible for repelling specific predators. Because using such chemicals is costly, animals with alternative cheaper defences are expected not to release such secretions when alternative options exist. In this study, we sought to determine the defensive mechanisms of the harvestman Discocyrtus invalidus, a heavy bodied species that bears a pair of repugnatorial glands. The spider Enoploctenus cyclothorax was used as the predator, and the cricket Gryllus sp. was used as a control. In a first set of experiments, the harvestmen were preyed upon significantly less than the crickets. In two other experiments, we found that harvestmen did not use their scent gland secretions to deter the predator. Moreover, results of a fourth experiment revealed that these spiders are not repelled by defensive secretions. Discocyrtus invalidus has a thick cuticle on the entire body: scanning electron micrographs revealed that only the mouth, the articulations of appendages and the tips of the legs are not covered by a hard integument. In a fifth experiment, we found that these spiders had difficulty piercing the harvestmen body. This is the first experimental evidence that a chemically defended arachnid does not use its scent gland secretions to repel a much larger predator but instead relies on its heavily built body. (c) 2010 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Parallel Dynamic Optimization of Steel Risers

This paper addresses the use of optimization techniques in the design of a steel riser. Two methods are used: the genetic algorithm, which imitates the process of natural selection, and the simulated annealing, which is based on the process of annealing of a metal. Both of them are capable of searching a given solution space for the best feasible riser configuration according to predefined criteria. Optimization issues are discussed, such as problem codification, parameter selection, definition of objective function, and restrictions. A comparison between the results obtained for economic and structural objective functions is made for a case study. Optimization method parallelization is also addressed. [DOI: 10.1115/1.4001955]

Rapid evolution towards equal sex ratios in a system with heterogamety

The equal sex ratios found in many species with heterogametic sex determination may be a consequence of selection for equality or the result of the Mendelian segregation of the two sex chromosomes. A lack of genetic variation in sex ratio in species with heterogamety has been the major obstacle in distinguishing between these two hypotheses. We overcome this obstacle by generating hybrids between two species of Drosophila. The resulting hybrid lines had biased sex ratios, allowing us to observe the evolution of sex ratio in replicate populations. Sex ratio converged towards 1:1 after 16 generations of natural selection. These changes in sex ratio were not due to differences in viability between the sexes and the loci underlying the variation in sex ratio were not sex-linked. Equal sex ratios may therefore be the result of natural selection as Fisher predicted.

Allele and genotype frequencies of polymorphic cytochromes P4502D6, 2C19 and 2E1 in Aborigines from Western Australia

The polymorphisms of the important xenobiotic metabolizing enzymes CYP2D6, CYP2C19 and CYP2E1 have been studied extensively in a large number of populations and show significant heterogeneity in the frequency of different alleles/genotypes and in the prevalence of the extensive and poor metabolizer phenotypes, Understanding of inter-ethnic differences in genotypes is important in prediction of either beneficial or adverse effects from therapeutic agents and other xenobiotics. Since no data were available for Australian Aborigines, we investigated the frequencies of alleles and genotypes for CYP2D6, CYP2C19 and CYP2E1 in a population living in the far north of Western Australia. Because of its geographical isolation, this population can serve as a model to study the impact of evolutionary forces on the distribution of different alleles for xenobiotic metabolizing enzymes. Twelve CYP2D6 alleles were analysed, The wild-type allele *1 was the most frequent (85.8%) and the non-functional alleles (*4, *5, *16) had an overall frequency of less than 10%. Only one subject (0.4%) was a poor metabolizer for CYP2D6 because of the genotype *5/*5, For CYP2C19, the frequencies of the *1 (wild-type) and the non-functional (*2 and *3) alleles were 50.2%, 35.5% and 14.3%, respectively. The combined CYP2C19 genotypes (*2/*2, *2/*3 or *3/*3) correspond to a predicted frequency of 25.6% for the CYP2C19 poor metabolizer phenotype, For CYP2E1, only one subject had the rare c2 allele giving an overall allele frequency of 0.2%. For CYP2D6 and CYP2C19, allele frequencies and predicted phenotypes differed significantly from those for Caucasians but were similar to those for Orientals indicating a close relationship to East Asian populations. Differences between Aborigines and Orientals in allele frequencies for CYP2D6*10 and CYP2E1 c2 may have arisen through natural selection, or genetic drift, respectively, Pharmacogenetics 11:69-76 (C) 2001 Lippincott Williams & Wilkins.

The advantages of theft over toil: The design inference and arguing from ignorance

Intelligent design theorist William Dembski has proposed an explanatory filter for distinguishing between events due to chance, lawful regularity or design. We show that if Dembski's filter were adopted as a scientific heuristic, some classical developments in science would not be rational, and that Dembski's assertion that the filter reliably identifies rarefied design requires ignoring the state of background knowledge. If background information changes even slightly, the filter's conclusion will vary wildly. Dembski fails to overcome Hume's objections to arguments from design.

Genetic covariance between indices of body condition and immunocompetence in a passerine bird

Background: Condition-dependence is a ubiquitous feature of animal life histories and has important implications for both natural and sexual selection. Mate choice, for instance, is typically based on condition-dependent signals. Theory predicts that one reason why condition-dependent signals may be special is that they allow females to scan for genes that confer high parasite resistance. Such explanations require a genetic link between immunocompetence and body condition, but existing evidence is limited to phenotypic associations. It remains unknown, therefore, whether females selecting males with good body condition simply obtain a healthy mate, or if they acquire genes for their offspring that confer high immunocompetence. Results: Here we use a cross-foster experimental design to partition the phenotypic covariance in indices of body condition and immunocompetence into genetic, maternal and environmental effects in a passerine bird, the zebra finch Taeniopygia guttata. We show that there is significant positive additive genetic covariance between an index of body condition and an index of cell-mediated immune response. In this case, genetic variance in the index of immune response explained 56% of the additive genetic variance in the index of body condition. Conclusion: Our results suggest that, in the context of sexual selection, females that assess males on the basis of condition-dependent signals may gain genes that confer high immunocompetence for their offspring. More generally, a genetic correlation between indices of body condition and imuunocompetence supports the hypothesis that parasite resistance may be an important target of natural selection. Additional work is now required to test whether genetic covariance exists among other aspects of both condition and immunocompetence.

The origin of the metazoan biphasic life cycle: New insights from an ancient phylum

The biphasic life cycle, characterised by metamorphosis from a pelagic larva to a benthic adult, is found throughout the Metazoa. So is sexual reproduction via eggs and sperm. Amidst a tangled web of hypotheses on the origin of metazoan biphasy, current weight of opinion lies with a simple, larva-like holopelagic ancestor that independently settled multiple times to incorporate a benthic phase into the life cycle. This school of thought derives from Haeckel's interpretation of the gastrula as the recapitulation of a gastrean ancestor that evolved via selection on a simple, planktonic hollow ball-of-cells to develop the capacity to feed. We suggest that a paradigm shift is required to accomodate accumulating evidence of the genomic and developmental complexity of the metazoan last common ancestor, which was likely to have already possessed a biphasic lifecycle. Here we incorporate recent evidence from basal metazoans, in particular poriferans, to argue that a more parsimonious theory of the origin of biphasy is as a direct consequence of sexual reproduction in an ancestral benthic adult form. The metazoan embryo can itself be considered the precursor to a biphasic life cycle, wherein the embryo represents one phase and the adult another. Embryos in the water column are subject to natural selection for longeveity and dispersal, which sets them on the evolutionary trajectory towards the crown metazoan planktonic larvae. This alternate view considers the conserved use of regulatory genes in disparate metazoans as a reflection of both the complexity of the LCA and the antiquity of the biphasic life cycle. It does not require that extant embryogenesis, including gastrulation, recapitulates evolution.

Absence of the HLA-G*0113N allele in Amerindian populations from the Brazilian Amazon region

The HLA-G gene is predominantly expressed at the maternal-fetal interface and has been associated with maternal-fetal tolerance. The HLA-G*0113N is a null allele defined by the insertion of a premature stop codon at exon 2, observed in a single Ghanaian individual. Likewise the G*0105N allele, the occurrence of the HL4-G*0113N in a population from an area with high pathogen load suggests that the reduced HLA-G expression in G*0113N heterozygous placentas could improve the intrauterine defense against infections. The presence of the G*0113N allele here was investigated in 150 Amerindians from five isolated tribes that inhabit the Central Amazon and in 295 admixed individuals from the State of Sao Paulo, Southeastern Brazil, previously genotyped for HLA-G. No copy of the G*0113N null allele was found in both population samples by exon 2 sequence-based analysis, reinforcing its restricted occurrence in Africa. (C) 2010 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Juvenile helping behaviour in the Dusky Moorhen, Gallinula tenebrosa

In Dusky Moorhens, Gallinula tenebrosa, helping behaviour maybe displayed by juveniles when groups contain offspring of different age classes. We investigated the frequency and amount of parental care provided by juvenile moorhens to younger siblings from subsequent same-year broods. In some social groups, juveniles provided up to 33% of the total number of feeds provided to chicks. Juveniles were observed to feed chicks when as young as six weeks of age, often while still receiving food from adults themselves. Low within-group relatedness and low reproductive costs associated with juvenile helping have important consequences for the cost-benefit ratio of helping behaviour in this species.

Evolutionary experiments on mate recognition in the Drosophila serrata species complex

It is becoming increasingly apparent that at least some aspects of the evolution of mate recognition may be amenable to manipulation in evolutionary experiments. Quantitative genetic analyses that focus on the genetic consequences of evolutionary processes that result in mate recognition evolution may eventually provide an understanding of the genetic basis of the process of speciation. We review a series of experiments that have attempted to determine the genetic basis of the response to natural and sexual selection on mate recognition in the Drosophila serrata species complex. The genetic basis of mate recognition has been investigated at three levels: (1) between the species of D. serrata and D. birchii using interspecific hybrids, (2) between populations of D. serrata that are sympatric and allopatric with respect to D. birchii, and (3) within populations of D. serrata. These experiments suggest that it may be possible to use evolutionary experiments to observe important events such as the reinforcement of mate recognition, or the generation of the genetic associations that are central to many sexual selection models.

Positive genetic correlation between female preference and offspring fitness

In many species, females display preferences for extreme male signal traits, but it has not been determined if such preferences evolve as a consequence of females gaining genetic benefits from exercising choice. If females prefer extreme male traits because they indicate male genetic quality that will enhance the fitness of offspring, a genetic correlation will evolve between female preference genes and genes that confer offspring fitness. We show that females of Drosophila serrata prefer extreme male cuticular hydrocarbon (CHC) blends, and that this preference affects offspring fitness. Female preference is positively genetically correlated with offspring fitness, indicating that females have gained genetic benefits from their choice of males. Despite male CHCs experiencing strong sexual selection, the genes underlying attractive CHCs also conferred lower offspring fitness, suggesting a balance between sexual selection and natural selection may have been reached in this population.