Diogo Meyer - Academia.edu (original) (raw)

Papers by Diogo Meyer

Frontiers in Immunology, 2020

This article deals with inter-relay power allocation for multiple-input multiple-output systems w... more This article deals with inter-relay power allocation for multiple-input multiple-output systems with multiple singleantenna relays. It is difficult to derive an optimal solution in a closed form for the case of multiple multi-antenna relays as well as the case of multiple single-antenna relays. In this article, we propose an approximate solution which is effective only for the case of multiple single-antenna relays. A key contribution of this article is a low complexity inter-relay power allocation method which is based on relay selection. This approach also reduces the feedback information of the gain factors of all the relays. An incremental greedy search algorithm is also proposed to further reduce the complexity of the relay selection process with negligible performance degradation. Simulations indicate that the performance is comparable to the optimal exhaustive search algorithm.

PLOS ONE

The American continent was the last to be occupied by modern humans, and native populations bear ... more The American continent was the last to be occupied by modern humans, and native populations bear the marks of recent expansions, bottlenecks, natural selection, and population substructure. Here we investigate how this demographic history has shaped genetic variation at the strongly selected HLA loci. In order to disentangle the relative contributions of selection and demography process, we assembled a dataset with genome-wide microsatellites and HLA-A,-B,-C, and-DRB1 typing data for a set of 424 Native American individuals. We find that demographic history explains a sizeable fraction of HLA variation, both within and among populations. A striking feature of HLA variation in the Americas is the existence of alleles which are present in the continent but either absent or very rare elsewhere in the world. We show that this feature is consistent with demographic history (i.e., the combination of changes in population size associated with bottlenecks and subsequent population expansions). However, signatures of selection at HLA loci are still visible, with significant evidence selection at deeper timescales for most loci and populations, as well as population differentiation at HLA loci exceeding that seen at neutral markers.

Encyclopedia of Life Sciences, 2008

The dominant selective force acting on protein-coding regions throughout the human genome is puri... more The dominant selective force acting on protein-coding regions throughout the human genome is purifying selection, which removes deleterious mutations. The fraction of substitutions that were positively selected, and can therefore be considered to be adaptive, can be estimated using methods based on comparisons of the relative amounts of change at two classes of sites – sites which if changed produce amino acid changes and sites which if changed do not lead to amino acid changes. Current estimates find very low estimates of adaptive evolution in protein-coding regions during human evolution. Keywords: purifying selection; adaptive evolution; human evolution; negative selection; positive selection

eLS, 2013

Evolutionary change can occur by nonadaptive processes, such as random genetic drift, and as a co... more Evolutionary change can occur by nonadaptive processes, such as random genetic drift, and as a consequence of selection on linked genetic variants. In addition, if selective regimes change over time, an allele currently at a high frequency because of past fitness advantage may be suboptimal for its present environment. Small effective population size along the human lineage increased the influence of drift, rendering mutations with slight effects on fitness effectively neutral. Demographic events like spatial expansions and population bottlenecks shape most of the genetic variation within and among modern populations. Natural selection itself may also contribute to nonadaptive or maladaptive change by increasing the frequency of linked deleterious variants. Also, certain maladaptive alleles may have increased in frequency because of compensating fitness advantages they provide. Key Concepts: Reduced effective population size along the human lineage led to an increase in the influence of genetic drift and a reduction in the efficacy of natural selection, especially for mutations with small selective effects. Evidence for this can be seen in comparisons of measures of natural selection in lineages having different effective population sizes. Genome-wide variation within and between human populations can be almost entirely explained by random drift and demographic forces other natural selection. Spatial expansions in human evolutionary history may cause gene surfing, in which low frequency alleles at the wave of advance can reach high frequencies and spread over large areas merely due to the effects of intense genetic drift. Nonadaptive gene surfing might be a better explanation than adaptive evolution for some high frequency, widespread genetic variants. Population bottlenecks in human evolutionary history can lead to increases in drift and reductions in the efficacy of purifying selection. This leads to an increase in the fraction of slightly deleterious mutations present in human populations that have experienced recent bottlenecks. Natural selection on alleles can result in nonadaptive shifts in the frequencies of alleles that are closely linked to them. Such linkage effects can lead to the increased frequencies of mildly deleterious alleles if they are linked to a beneficial variant, and can interfere with the effectiveness of adaptive evolution in promoting an advantageous allele if it is linked to a deleterious allele. Caution should be exercised in interpreting patterns of genetic variation in human populations as being adaptive without thoroughly ruling out nonadaptive explanations. Keywords: population genetics; evolution; natural selection; positive selection; purifying selection; human evolution; gene surfing; adaptation; linkage; effective population size; genetic drift; nonadaptive

Filosofia E Historia Da Biologia, 2013

Resumo: Lidar com o embate entre perspectivas criacionistas e evolucionistas é parte da realidade... more Resumo: Lidar com o embate entre perspectivas criacionistas e evolucionistas é parte da realidade de muitos professores de biologia. Neste ensaio buscamos caracterizar esse confronto, sugerindo que ele não pode ser caracterizado como um "debate". A seguir argumentamos que a perspectiva criacionista, quando apresentada como alternativa excludente à evolução, acaba por trazer prejuízos para o ensino de ciências que vão muito além do ensino da biologia. No final oferecemos algumas sugestões para ajudar professores a se posicionarem diante de perspectivas criacionistas. Palavras-chave: evolução; criacionismo; ensino de ciências; debates científicos What is at stake in the confrontation between creationism and evolution Abstract: Dealing with the debate involving the clash of evolutionist and creationist perspectives is part of the daily life of many science teachers. In this essay we seek to understand this conflict, suggesting that it is not a true "debate". Next, we argue that the creationist perspective, when presented as an alternative that excludes evolutionary explanations, ultimately does as much harm to science education as a whole as it does to the teaching of

F1000Research, 2014

Population data file consists of:-a 'header' block with overall information about that population... more Population data file consists of:-a 'header' block with overall information about that population;-a 'data' block where each line contains the population name, sample identifier and the alleles at each locus-each block starts with the list of valid field names for each column in that block. e.g. an edited extract from 3. Data and input file format The driver script generates overall summary and diversity indices (see below) and calls on one or more of the following modules (configurable by user).

As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics ... more As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~ 2 million are absent from large public databases. WGS enabled identifying ~ 2,000 novel mobile element insertions, nearly 5 Mb of genomic segments absent from human genome reference, and over 140 novel alleles from HLA genes. We reclassified and curated nearly four hundred variant's pathogenicity assertions in genes associated with dominantly inherited Mendelian disorders and calculated the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observed that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variat...

Contrastes. Revista Internacional de Filosofía, 2013

ABSTRACTThe view of the gene as a structural and functional unit has been increasingly challenged... more ABSTRACTThe view of the gene as a structural and functional unit has been increasingly challenged by findings mostly resulting from eukaryote research. We can classify these challenges in three kinds: (i) one-to-many correspondences between DNA segments and RNAs/polypeptides (as, for instance, in alternative splicing); (ii) many-to-one correspondences between DNA segments and RNAs/polypeptides (as in genomic rearrangements, say, those involved in the generation of diversity in lymphocyte antigen receptors); (iii) lack of correspondence between DNA segments and RNAs/polypeptides (as, for example, in mRNA editing). However, even if a single definition of a gene may not be a realistic (or even helpful) goal, being able to have different definitions connected to each other –operationally and theoretically– is of central importance.KEYWORDSGENE CONCEPT, DEFINITION, DNARESUMENLa idea según la cual el gen es una unidad estructural y funcional se ha visto cada vez más cuestionada a causa de...

Balancing selection maintains advantageous diversity in populations through various mechanisms. W... more Balancing selection maintains advantageous diversity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe theNon-Central Deviation(NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test.NCDcan be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, andNCD2has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgrou...

Proceedings of the National Academy of Sciences of the United States of America, Feb 28, 2017

When humans moved from Asia toward the Americas over 18,000 y ago and eventually peopled the New ... more When humans moved from Asia toward the Americas over 18,000 y ago and eventually peopled the New World they encountered a new environment with extreme climate conditions and distinct dietary resources. These environmental and dietary pressures may have led to instances of genetic adaptation with the potential to influence the phenotypic variation in extant Native American populations. An example of such an event is the evolution of the fatty acid desaturases (FADS) genes, which have been claimed to harbor signals of positive selection in Inuit populations due to adaptation to the cold Greenland Arctic climate and to a protein-rich diet. Because there was evidence of intercontinental variation in this genetic region, with indications of positive selection for its variants, we decided to compare the Inuit findings with other Native American data. Here, we use several lines of evidence to show that the signal of FADS-positive selection is not restricted to the Arctic but instead is bro...

Scientific reports, Oct 6, 2016

Human pluripotent stem cells (hPSCs) may significantly improve drug development pipeline, serving... more Human pluripotent stem cells (hPSCs) may significantly improve drug development pipeline, serving as an in vitro system for the identification of novel leads, and for testing drug toxicity. Furthermore, these cells may be used to address the issue of differential drug response, a phenomenon greatly influenced by genetic factors. This application depends on the availability of hPSC lines from populations with diverse ancestries. So far, it has been reported that most lines of hPSCs derived worldwide are of European or East Asian ancestries. We have established 23 lines of hPSCs from Brazilian individuals, and we report the analysis of their genomic ancestry. We show that embryo-derived PSCs are mostly of European descent, while induced PSCs derived from participants of a national-wide Brazilian cohort study present high levels of admixed European, African and Native American genomic ancestry. Additionally, we use high density SNP data and estimate local ancestries, particularly those...

Immunogenetics, 2015

Supertypes are groups of human leukocyte antigen (HLA) alleles which bind overlapping sets of pep... more Supertypes are groups of human leukocyte antigen (HLA) alleles which bind overlapping sets of peptides due to sharing specific residues at the anchor positions-the B and F pockets-of the peptide-binding region (PBR). HLA alleles within the same supertype are expected to be functionally similar, while those from different supertypes are expected to be functionally distinct, presenting different sets of peptides. In this study, we applied the supertype classification to the HLA-A and HLA-B data of 55 worldwide populations in order to investigate the effect of natural selection on supertype rather than allelic variation at these loci. We compared the nucleotide diversity of the B and F pockets with that of the other PBR regions through a resampling procedure and compared the patterns of within-population heterozygosity (He) and between-population differentiation (G ST) observed when using the supertype definition to those estimated when using randomized groups of alleles. At HLA-A, low levels of variation are observed at B and F pockets and randomized He and G ST do not differ from the observed data. By contrast, HLA-B concentrates most of the differences between supertypes, the B pocket showing a particularly high level of variation. Moreover, at HLA-B, the reassignment of alleles into random groups does not reproduce the patterns of population differentiation observed with supertypes. We thus conclude that differently from HLA-A, for which supertype and allelic variation show similar patterns of nucleotide diversity within and between populations, HLA-B has likely evolved through specific adaptations of its B pocket to local pathogens.

PyPop (Python for Population Genomics) is an environment developed at UC Berkeley for doing large... more PyPop (Python for Population Genomics) is an environment developed at UC Berkeley for doing large-scale population genetic analyses including:• conformity to Hardy-Weinberg expectations• tests for balancing or directional selection• estimates of haplotype frequencies and measures and tests of signiﬁcance for linkage disequilib-rium (LD)

Human biology, 2014

This article deals with the estimation of inbreeding and substructure levels in a set of 10 (late... more This article deals with the estimation of inbreeding and substructure levels in a set of 10 (later regrouped as eight) African-derived quilombo communities from the Ribeira River Valley in the southern portion of the state of São Paulo, Brazil. Inbreeding levels were assessed through F-values estimated from the direct analysis of genealogical data and from the statistical analysis of a large set of 30 molecular markers. The levels of population substructure found were modest, as was the degree of inbreeding: in the set of all communities considered together, F-values were 0.00136 and 0.00248 when using raw and corrected data from their complete genealogical structures, respectively, and 0.022 and 0.036 when using the information taken from the statistical analysis of all 30 loci and of 14 single-nucleotide polymorphic loci, respectively. The overall frequency of consanguineous marriages in the set of all communities considered together was ∼2%. Although modest, the values of the est...

Journal of Ornithology, 2013

Studies of Atlantic forest (AF) organisms suggest that the historical dynamics of the forest cove... more Studies of Atlantic forest (AF) organisms suggest that the historical dynamics of the forest cover produced demographically stable populations in its central region and unstable populations in the southern regions. We studied the mitochondrial phylogeographic structure of an AF passerine, the Greenish Schiffornis Schiffornis virescens (Tityridae), and evaluated questions related to the history of the AF. We analyzed cytochrome b and control region sequences of the mitochondrial genome by traditional phylogenetic and population genetic methods based on summary statistics. In addition, we used coalescent simulations to evaluate specific models of evolution of the populations of S. virescens. The results did not support phylogeographic partitions of the genetic variability of S. virescens. The overall Ust was = 0.32 and gene flow between regions was moderate to high. The analyses suggested that the total population of S. virescens suffered a bottleneck followed by a demographic expansion in the late Pleistocene. The bottleneck might have contributed to the extinction of intraspecific lineages, and hence to the observed lack of a strong phylogeographic pattern and low genetic diversity. Our results suggest that some AF taxa have had all their populations similarly affected by the recent history of the biome, contrary to what has been revealed from most of the other phylogeographic studies in the region and as suggested by a model of AF refuges (the Carnaval-Moritz model). We suggest that the response of organisms to common histories may be idiosyncratic, and predictions about the history of the biome should take into account ecological characteristics and distribution of each specific taxa. Keywords Atlantic forest Á Phylogeography Á mtDNA Á Schiffornis Á Historical demography Zusammenfassung Communicated by J. Fjeldså.

Tissue Antigens, 2004

The allelic and haplotypic diversity of the HLA-A, HLA-B, and HLA-C loci was investigated in 852 ... more The allelic and haplotypic diversity of the HLA-A, HLA-B, and HLA-C loci was investigated in 852 subjects from five sub-Saharan populations from Kenya (Nandi and Luo), Mali (Dogon), Uganda, and Zambia. Distributions of genotypes at all loci and in all populations fit Hardy-Weinberg equilibrium expectations. There was not a single allele predominant at any of the loci in these populations, with the exception of A*3002 [allele frequency (AF) ¼ 0.233] in Zambians and Cw*1601 (AF ¼ 0.283) in Malians. This distribution was consistent with balancing selection for all class I loci in all populations, which was evidenced by the homozygosity F statistic that was less than that expected under neutrality. Only in the A locus in Zambians and the C locus in Malians, the AF distribution was very close to neutrality expectations. There were six instances in which there were significant deviations of allele distributions from neutrality in the direction of balancing selection. All allelic lineages from each of the class I loci were found in all the African populations. Several alleles of these loci have intermediate frequencies (AF ¼ 0.020-0.150) and seem to appear only in the African populations. Most of these alleles are widely distributed in the African continent and their origin may predate the separation of linguistic groups. In contrast to native American and other populations, the African populations do not seem to show extensive allelic diversification within lineages, with the exception of the groups of alleles A*02, A*30, B*57, and B*58. The alleles of human leukocyte antigen (HLA)-B are in strong linkage disequilibrium (LD) with alleles of the C locus, and the sets of B/C haplotypes are found in several populations. The associations between A alleles with C-blocks are weaker, and only a few A/B/C haplotypes (A*0201-B*4501-Cw*1601; A*2301-B*1503-Cw*0202; A*7401-B* 1503-Cw*0202; A*2902-B*4201-Cw*1701; A*3001-B*4201-Cw*1701; and A*3601-B*5301-Cw*0401) are found in multiple populations with intermediate frequencies [haplotype frequency (HF) ¼ 0.010-0.100]. The strength of the LD associations between alleles of HLA-A and HLA-B loci and those of HLA-B and HLA-C loci was on average of the same or higher magnitude as those observed in other non-African populations for the same pairs of loci. Comparison of the genetic distances measured by the distribution of alleles at the HLA class I loci in the sub-Saharan populations included in this and other studies indicate that the Luo population from western Kenya has the closest distance with virtually all sub-Saharan population so far studied for HLA-A, a finding consistent with the putative origin of modern humans in East Africa. In all African populations, the genetic distances between each other are greater than those observed between European populations. The remarkable current allelic and haplotypic diversity in the HLA system as well as their variable distribution in different sub-Saharan populations is probably the result of evolutionary forces and environments that have acted on each individual population or in their ancestors. In this regard, the genetic diversity of the HLA system in African populations poses practical challenges for the design of T-cell vaccines and for the transplantation medical community to find HLA-matched unrelated donors for patients in need of an allogeneic transplant.

Tissue Antigens, 2007

The 14th International HLA (human leukocyte antigen) Immunogenetics Workshop (14th-IHIWS) Biostat... more The 14th International HLA (human leukocyte antigen) Immunogenetics Workshop (14th-IHIWS) Biostatistics and Anthropology/Human Genetic Diversity project continues the population sampling, genotype data generation, and biostatistic analyses of the 13th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Component, with the overall goal of further characterizing global HLA allele and haplotype diversity and better describing the relationships between major histocompatibility complex diversity, geography, linguistics, and population history. Since the 13th Workshop, new investigators have and continue to be recruited to the project and new highresolution class I and class II genotype data are being generated for 112 population samples from around the world.

Journal of the Marine Biological Association of the United Kingdom, 2009

The South American fur seal,Arctocephalus australis, was one of the earliest otariid seals to be ... more The South American fur seal,Arctocephalus australis, was one of the earliest otariid seals to be exploited by humans: at least 6000 years ago on the Atlantic coast and 4000 on the Pacific coast of South America. More than 750,000 fur seals were killed in Uruguay until 1991. However, a climatological phenomenon—the severe 1997–1998 El Niño Southern Oscillation (ENSO)—was responsible for the decline of 72% of the Peruvian fur seal population due to starvation as a consequence of warming of sea-surface temperatures and primary productivity reduction. Currently, there is no precise information on global population size or on the species' conservation status. The present study includes the first bottleneck test for the Pacific and Atlantic populations ofA. australisbased on the analysis of seven microsatellite loci. Genetic bottleneck compromises the evolutionary potential of a population to respond to environmental changes. The perspective becomes even more alarming due to current g...

PLoS ONE, 2011

A total of 172 persons from nine South Amerindian, three African and one Eskimo populations were ... more 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 59and 39flanking 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.

Molecular Ecology, 2010

The hypothesis of gene flow between species with large differences in chromosome numbers has rare... more The hypothesis of gene flow between species with large differences in chromosome numbers has rarely been tested in the wild, mainly because species of different ploidy are commonly assumed to be reproductively isolated from each other because of instantaneous and strong postzygotic barriers. In this study, a broad-scale survey of molecular variation was carried out between two orchid species with different ploidy levels: Epidendrum fulgens (2n = 2x = 24 chromosomes) and Epidendrum puniceoluteum (2n = 4x = 52 chromosomes). To test the strength of their reproductive barriers, we investigated the distribution of genetic variation in sympatric and allopatric populations of these two species and conducted crossing experiments. Nuclear and plastid microsatellite loci were used to genotype 463 individuals from eight populations across the geographical range of both species along the Brazilian coastal plain. All six sympatric populations analysed presented hybrid zones, indicating that hybridization between E. fulgens and E. puniceoluteum is a common phenomenon. Bayesian assignment analysis detected the presence of F 1 and F 2 individuals and also signs of introgression, demonstrating a high potential for interspecific gene flow. Introgression occurs preferentially from E. fulgens to E. puniceoluteum. Pure parental individuals of both species display strong genotype-habitat associations, indicating that environment-dependent selection could be acting in all hybrid zones. This study suggests that hybridization and introgression are evolutionary processes playing a role in the diversification of Epidendrum and indicates the importance of investigations of hybrid zones in understanding reproductive barriers and speciation processes in Neotropical orchid species.