Genes mirror geography within Europe.

Understanding the genetic structure of human populations is of fundamental interest to medical, forensic and anthropological sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation and suggest the potential to use large samples to uncover variation among closely spaced populations. Here we characterize genetic variation in a sample of 3,000 European individuals genotyped at over half a million variable DNA sites in the human genome. Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans. The results emphasize that when mapping the genetic basis of a disease phenotype, spurious associations can arise if genetic structure is not properly accounted for. In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy-often to within a few hundred kilometres.

Modeling the forensic two-trace problem with Bayesian networks

The forensic two-trace problem is a perplexing inference problem introduced by Evett (J Forensic Sci Soc 27:375-381, 1987). Different possible ways of wording the competing pair of propositions (i.e., one proposition advanced by the prosecution and one proposition advanced by the defence) led to different quantifications of the value of the evidence (Meester and Sjerps in Biometrics 59:727-732, 2003). Here, we re-examine this scenario with the aim of clarifying the interrelationships that exist between the different solutions, and in this way, produce a global vision of the problem. We propose to investigate the different expressions for evaluating the value of the evidence by using a graphical approach, i.e. Bayesian networks, to model the rationale behind each of the proposed solutions and the assumptions made on the unknown parameters in this problem.

Source inference of exogenous gamma-hydroxybutyric acid (GHB) administered to humans by means of carbon isotopic ratio analysis: novel perspectives regarding forensic investigation and intelligence issues.

γ-Hydroxybutyric acid (GHB) is an endogenous short-chain fatty acid popular as a recreational drug due to sedative and euphoric effects, but also often implicated in drug-facilitated sexual assaults owing to disinhibition and amnesic properties. Whilst discrimination between endogenous and exogenous GHB as required in intoxication cases may be achieved by the determination of the carbon isotope content, such information has not yet been exploited to answer source inference questions of forensic investigation and intelligence interests. However, potential isotopic fractionation effects occurring through the whole metabolism of GHB may be a major concern in this regard. Thus, urine specimens from six healthy male volunteers who ingested prescription GHB sodium salt, marketed as Xyrem(®), were analysed by means of gas chromatography/combustion/isotope ratio mass spectrometry to assess this particular topic. A very narrow range of δ(13)C values, spreading from -24.810/00 to -25.060/00, was observed, whilst mean δ(13)C value of Xyrem(®) corresponded to -24.990/00. Since urine samples and prescription drug could not be distinguished by means of statistical analysis, carbon isotopic effects and subsequent influence on δ(13)C values through GHB metabolism as a whole could be ruled out. Thus, a link between GHB as a raw matrix and found in a biological fluid may be established, bringing relevant information regarding source inference evaluation. Therefore, this study supports a diversified scope of exploitation for stable isotopes characterized in biological matrices from investigations on intoxication cases to drug intelligence programmes.

Evolutionary genetics of arbuscular mycorrhizal fungi - causes and consequences of multiple genomes in Glomus intraradices

Résumé Les champignons endomycorhiziens arbusculaires (CEA) forment des symbioses avec la plupart des plantes terrestres. Les CEA influencent la croissance des plantes et la biodiversité. Ils sont supposés avoir évolué de manière asexuée pendant au moins 400 millions d'années et aucune diversification morphologique majeure n'a été constatée. Pour ces raisons, les CEA sont considérés comme d'anciens asexués. Très peu d'espèces sont connues actuellement. Les individus de ces champignons contiennent des noyaux génétiquement différents dans un cytoplasme continu. La signification évolutive, la variabilité et la maintenance des génomes multiples au sein des individus sont inconnues. Ce travail a démontré qu'une population du CEA Glomus intraradices est génétiquement très variable. Nous avons conclu que les plantes hôtes plutôt que la différenciation géographique devraient être responsables de cette grande diversité. Puis nous avons cherché l'existence de recombinaison entre génotypes dans une population. Nous avons détecté un groupe recombinant au sein de la population, ce qui met en doute l'état d'anciens asexués des CEA. Nous avons également détecté l'occurrence de fusions d'hyphes et l'échange de noyaux entre isolats génétiquement différents. La descendance hybride issue de cet échange était viable et distincte phénotypiquement des isolats parentaux. En résumé, ce travail identifie des événements cruciaux dans le cycle de vie des CEA qui ont le potentiel d'influencer l'évolution de génomes multiples. L'étude des conséquences de ces événements sur les interactions avec les plantes hôtes pourrait éclaircir significativement la compréhension de la symbiose entre plantes et CEA. Abstract Arbuscular mycorrhizal fungi (AMF) are important symbionts of most land plants. AMF influence plant growth and biodiversity. Very few extant species are described. AMF are thought to have evolved asexually for at least 400 million years and no major morphological diversification has occurred. Due to these reasons, they were termed `ancient asexuals'. Fungal individuals harbour genetically different nuclei in a continuous cytoplasm. The variability, maintenance and evolutionary significance of multiple genomes within individuals are unknown. This work showed that a population of the AMF Glomus intraradices harbours very high genetic diversity. We concluded that host plants rather than geographic differentiation were responsible for this diversity. Furthermore, we investigated whether recombination occurred among genotypes of a G. intraradices population. The identification of a core group of recombining genotypes in the population refutes the assumption of ancient asexuality in AMF. We found that genetically different isolates can form hyphal fusions and exchange nuclei. The hybrid progeny produced by the exchange was viable and phenotypically distinct from the parental isolates. Taken together, this work provided evidence for key events in the AMF life cycle, that influence the evolution of multiple genomes. Studying the consequences of these events on the interaction with host plants may significantly further the understanding of the AMF-plant symbiosis.

Influence of photoperiod on body weight and depth of burrowing in larvae of Chrysomya megacephala (Fabricius) (Diptera, Calliphoridae) and implications for forensic entomology

Blowflies use discrete, ephemeral breeding sites for larval nutrition. After exhaustion of the food supply, the larvae disperse in search of sites to pupate or to seek other sources of food in a process known as post-feeding larval dispersal. In this study, some of the most important aspects of this process were investigated in larvae of the blowflies Chrysomya megacephala exposed to a variety of light: dark (LD) cycles (0:0 h, 12:12 h and 24:0 h) and incubated in tubes covered with vermiculite. For each pupa, the body weight and depth of burrowing were determined. Statistical tests were used to examine the relationship of depth of burrowing and body weight to photoperiod at which burrowing occurred. The study of burial behavior in post-feeding larval dispersing can be useful for estimating the postmortem interval (PMI) of human corpses in forensic medicine.

Use of forensic investigations in anti-doping

The fight against doping is mainly focused on direct detection, using analytical methods for the detection of doping agents in biological samples. However, the World Anti-Doping Code also defines doping as possession, administration or attempted administration of prohibited substances or methods, trafficking or attempted trafficking in any prohibited substance or methods. As these issues correspond to criminal investigation, a forensic approach can help assessing potential violation of these rules.In the context of a rowing competition, genetic analyses were conducted on biological samples collected in infusion apparatus, bags and tubing in order to obtain DNA profiles. As no database of athletes' DNA profiles was available, the use of information from the location detection as well as contextual information were key to determine a population of suspected athletes and to obtain reference DNA profiles for comparison.Analysis of samples from infusion systems provided 8 different DNA profiles. The comparison between these profiles and 8 reference profiles from suspected athletes could not be distinguished.This case-study is one of the first where a forensic approach was applied for anti-doping purposes. Based on this investigation, the International Rowing Federation authorities decided to ban not only the incriminated athletes, but also the coaches and officials for 2 years.

Use of forensic investigations in anti-doping.

The fight against doping is mainly focused on direct detection, using analytical methods for the detection of doping agents in biological samples. However, the World Anti-Doping Code also defines doping as possession, administration or attempted administration of prohibited substances or methods, trafficking or attempted trafficking in any prohibited substance or methods. As these issues correspond to criminal investigation, a forensic approach can help assessing potential violation of these rules. In the context of a rowing competition, genetic analyses were conducted on biological samples collected in infusion apparatus, bags and tubing in order to obtain DNA profiles. As no database of athletes' DNA profiles was available, the use of information from the location detection as well as contextual information were key to determine a population of suspected athletes and to obtain reference DNA profiles for comparison. Analysis of samples from infusion systems provided 8 different DNA profiles. The comparison between these profiles and 8 reference profiles from suspected athletes could not be distinguished. This case-study is one of the first where a forensic approach was applied for anti-doping purposes. Based on this investigation, the International Rowing Federation authorities decided to ban not only the incriminated athletes, but also the coaches and officials for 2 years.

Key to the adults of the most common forensic species of Diptera in South America

Flies (Diptera, blow flies, house flies, flesh flies, horse flies, cattle flies, deer flies, midges and mosquitoes) are among the four megadiverse insect orders. Several species quickly colonize human cadavers and are potentially useful in forensic studies. One of the major problems with carrion fly identification is the lack of taxonomists or available keys that can identify even the most common species sometimes resulting in erroneous identification. Here we present a key to the adults of 12 families of Diptera whose species are found on carrion, including human corpses. Also, a summary for the most common families of forensic importance in South America, along with a key to the most common species of Calliphoridae, Muscidae, and Fanniidae and to the genera of Sarcophagidae are provided. Drawings of the most important characters for identification are also included.

Insects of forensic importance from Rio Grande do Sul state in southern Brazil

The experiment was conducted throughout the year 2005, at the Universidade Federal de Pelotas campus. The objectives of the study were to analyze the decomposition of rabbit (Oryctolagus cunniculus L.) with mean weight 2.67 Kg carcass and describe the interaction of insects acting on it, as well as the insect's potential use in legal medicine. We collected 5.239 insect specimens; 1.827 of them were obtained from larvae collected from carcasses and reared. The specimens were identified and 20 species were of forensic importance. The species Lucilia eximia (Wiedemann, 1819) and Chrysomya albiceps (Wiedemann, 1819) (Diptera, Calliphoridae) were better indicators of post-mortem interval (PMI) because they occurred in all seasons and were the first to reach the carcass. Hemilucilia semidiaphana (Rondani, 1850), H. segmentaria (Fabricius, 1805) (Diptera, Calliphoridae), Muscina stabulans (Fallén, 1817) and Synthesiomyia nudiseta (Wulp, 1883) (Diptera, Muscidae) can disclose death time because they occur only in certain months of the year. Oxyletrum discicolle (Brullé, 1840) (Coleoptera, Silphidae) and Dermestes maculates De Geer, 1774 (Coleoptera, Desmestidae) were found in advanced stages of decomposition.

Diagnosis and key of the main families and species of South American Coleoptera of forensic importance

The objective of this paper is to provide diagnosis and keys of the families and species, with illustrations of the main groups. A table of all related species recorded from South America is presented, including the substrate in which they were collected and their geographical distribution. The list comprises 221 species included in 15 families, of which 70% of the species are from Brazil. Scarabaeidae is the most diverse family with 121 species, followed by Staphylinidae with 68. Also we provide one database of Coleoptera species associated with carcasses in South America.

Phylogenetic analyses of C4 photosynthesis evolution in grasses: genetics of convergence and convergence of genes

Summary : During the evolutionary diversification of organisms, similar ecological constraints led to the recurrent appearances of the same traits (phenotypes) in distant lineages, a phenomenon called convergence. In most cases, the genetic origins of the convergent traits remain unknown, but recent studies traced the convergent phenotypes to recurrent alterations of the same gene or, in a few cases, to identical genetic changes. However, these cases remain anecdotal and there is a need for a study system that evolved several times independently and whose genetic determinism is well resolved and straightforward, such as C4 photosynthesis. This adaptation to warm environments, possibly driven by past atmospheric CO2 decreases, consists in a CO2-concentrating pump, created by numerous morphological and biochemical novelties. All genes encoding C4 enzymes already existed in C3 ancestors, and are supposed to have been recruited through gene duplication followed by neo-functionalization, to acquire the cell specific expression pattern and altered kinetic properties that characterize Ca-specific enzymes. These predictions have so far been tested only in species-poor and ecologically marginal C4 dicots. The monocots, and especially the grass family (Poaceae), the most important C4 family in terms of species number, ecological dominance and economical importance, have been largely under-considered as suitable study systems. This thesis aimed at understanding the evolution of the C4 trait in grasses at a molecular level and to use the genetics of C4 photosynthesis to infer the evolutionary history of the C4 phenotype and its driving selective pressures. A molecular phylogeny of grasses and affiliated monocots identified 17 to 18 independent acquisitions of the C4 pathway in the grass family. A relaxed molecular clock was used to date these events and the first C4 evolution was estimated in the Chloridoideae subfamily, between 32-25 million years ago, at a period when atmospheric CO2 abruptly declined. Likelihood models showed that after the COZ decline the probability of evolving the C4 pathway strongly increased, confirming low CO2 as a likely driver of C4 photosynthesis evolution. In order to depict the genetic changes linked to the numerous C4 origins, genes encoding phopshoenolpyruvate carboxylase (PEPC), the key-enzyme responsible for the initial fixation of atmospheric CO2 in the C4 pathway, were isolated from a large sample of C3 and C4 grasses. Phylogenetic analyses were used to reconstruct the evolutionary history of the PEPC multigene family and showed that the evolution of C4-specific PEPC had been driven by positive selection on 21 codons simultaneously in up to eight C4 lineages. These selective pressures led to numerous convergent genetic changes in many different C4 clades, highlighting the repeatability of some evolutionary processes, even at the molecular level. PEPC C4-adaptive changes were traced and used to show multiple appearances of the C, pathway in clades where species tree inferences were unable to differentiate multiple C4 appearances and a single appearance followed by C4 to C3 reversion. Further investigations of genes involved in some of the C4 subtypes only (genes encoding decarboxylating enzymes NADP-malic enzyme and phosphoenolpyruvate carboxykinase) showed that these C4-enzymes also evolved through strong positive selection and underwent parallel genetic changes during the different Ca origins. The adaptive changes on these subtype-specific C4 genes were used to retrace the history of the C4-subtypes phenotypes, which revealed that the evolution of C4-PEPC and C4-decarboxylating enzymes was in several cases disconnected, emphasizing the multiplicity of the C4 trait and the gradual acquisition of the features that create the CO2-pump. Finally, phylogenetic analyses of a gene encoding the Rubisco (the enzyme responsible for the fixation of CO2 into organic compounds in all photosynthetic organisms) showed that C4 evolution switched the selective pressures on this gene. Five codons were recurrently mutated to adapt the enzyme kinetics to the high CO2 concentrations of C4 photosynthetic cells. This knowledge could be used to introgress C4-like Rubisco in C3 crops, which could lead to an increased yield under predicted future high CO2 atmosphere. Globally, the phylogenetic framework adopted during this thesis demonstrated the widespread occurrence of genetic convergence on C4-related enzymes. The genetic traces of C4 photosynthesis evolution allowed reconstructing events that happened during the last 30 million years and proved the usefulness of studying genes directly responsible for phenotype variations when inferring evolutionary history of a given trait. Résumé Durant la diversification évolutive des organismes, des pressions écologiques similaires ont amené à l'apparition récurrente de certains traits (phénotypes) dans des lignées distantes, un phénomène appelé évolution convergente. Dans la plupart des cas, l'origine génétique des traits convergents reste inconnue mais des études récentes ont montré qu'ils étaient dus dans certains cas à des changements répétés du même gène ou, dans de rares cas, à des changements génétiques identiques. Malgré tout, ces cas restent anecdotiques et il y a un réel besoin d'un système d'étude qui ait évolué indépendamment de nombreuses fois et dont le déterminisme génétique soit clairement identifié. La photosynthèse dite en Ça répond à ces critères. Cette adaptation aux environnements chauds, dont l'évolution a pu être encouragé par des baisses passées de la concentration atmosphérique en CO2, est constituée de nombreuses nouveautés morphologiques et biochimiques qui créent une pompe à CO2. La totalité des gènes codant les enzymes Ç4 étaient déjà présents dans les ancêtres C3. Leur recrutement pour la photosynthèse Ç4 est supposé s'être fait par le biais de duplications géniques suivies par une néo-fonctionnalisation pour leur conférer l'expression cellule-spécifique et les propriétés cinétiques qui caractérisent les enzymes C4. Ces prédictions n'ont jusqu'à présent été testées que dans des familles C4 contenant peu d'espèces et ayant un rôle écologique marginal. Les graminées (Poaceae), qui sont la famille C4 la plus importante, tant en termes de nombre d'espèces que de dominance écologique et d'importance économique, ont toujours été considérés comme un système d'étude peu adapté et ont fait le sujet de peu d'investigations évolutives. Le but de cette thèse était de comprendre l'évolution de la photosynthèse en C4 chez les graminées au niveau génétique et d'utiliser les gènes pour inférer l'évolution du phénotype C4 ainsi que les pressions de sélection responsables de son évolution. Une phylogénie moléculaire de la famille des graminées et des monocotylédones apparentés a identifié 17 à 18 acquisitions indépendantes de la photosynthèse chez les graminées. Grâce à une méthode d'horloge moléculaire relâchée, ces évènements ont été datés et la première apparition C4 a été estimée dans la sous-famille des Chloridoideae, il y a 32 à 25 millions d'années, à une période où les concentrations atmosphériques de CO2 ont décliné abruptement. Des modèles de maximum de vraisemblance ont montré qu'à la suite du déclin de CO2, la probabilité d'évoluer la photosynthèse C4 a fortement augmenté, confirmant ainsi qu'une faible concentration de CO2 est une cause potentielle de l'évolution de la photosynthèse C4. Afin d'identifier les mécanismes génétiques responsables des évolutions répétées de la photosynthèse C4, un segment des gènes codant pour la phosphoénolpyruvate carboxylase (PEPC), l'enzyme responsable de la fixation initiale du CO2 atmosphérique chez les plantes C4, ont été séquencés dans une centaine de graminées C3 et C4. Des analyses phylogénétiques ont permis de reconstituer l'histoire évolutive de la famille multigénique des PEPC et ont montré que l'évolution de PEPC spécifiques à la photosynthèse Ça a été causée par de la sélection positive agissant sur 21 codons, et ce simultanément dans huit lignées C4 différentes. Cette sélection positive a conduit à un grand nombre de changements génétiques convergents dans de nombreux clades différents, ce qui illustre la répétabilité de certains phénomènes évolutifs, et ce même au niveau génétique. Les changements sur la PEPC liés au C4 ont été utilisés pour confirmer des évolutions indépendantes du phénotype C4 dans des clades où l'arbre des espèces était incapable de différencier des apparitions indépendantes d'une seule apparition suivie par une réversion de C4 en C3. En considérant des gènes codant des protéines impliquées uniquement dans certains sous-types C4 (deux décarboxylases, l'enzyme malique à NADP et la phosphoénolpyruvate carboxykinase), des études ultérieures ont montré que ces enzymes C4 avaient elles-aussi évolué sous forte sélection positive et subi des changements génétiques parallèles lors des différentes origines de la photosynthèse C4. Les changements adaptatifs sur ces gènes liés seulement à certains sous-types C4 ont été utilisés pour retracer l'histoire des phénotypes de sous-types C4, ce qui a révélé que les caractères formant le trait C4 ont, dans certains cas, évolué de manière déconnectée. Ceci souligne la multiplicité du trait C4 et l'acquisition graduelle de composants participant à la pompe à CO2 qu'est la photosynthèse C4. Finalement, des analyses phylogénétiques des gènes codant pour la Rubisco (l'enzyme responsable de la fixation du CO2 en carbones organiques dans tous les organismes photosynthétiques) ont montré que l'évolution de la photosynthèse Ça a changé les pressions de sélection sur ce gène. Cinq codons ont été mutés de façon répétée afin d'adapter les propriétés cinétiques de la Rubisco aux fortes concentrations de CO2 présentes dans les cellules photosynthétiques des plantes C4. Globalement, l'approche phylogénétique adoptée durant cette thèse de doctorat a permis de démontré des phénomène fréquents de convergence génétique sur les enzymes liées à la photosynthèse C4. Les traces génétiques de l'évolution de la photosynthèse C4 ont permis de reconstituer des évènements qui se sont produits durant les derniers 30 millions d'années et ont prouvé l'utilité d'étudier des gènes directement responsables des variations phénotypiques pour inférer l'histoire évolutive d'un trait donné.

Pictorial identification key for species of Sarcophagidae (Diptera) of potential forensic importance in southern Brazil

Pictorial identification key for species of Sarcophagidae (Diptera) of potential forensic importance in southern Brazil. Species of the subfamily Sarcophaginae are important to forensic entomology due to their necrophagous habits. This contribution presents a pictorial key for the identification of 22 Sarcophaginae species in 10 genera that are commonly found in southern Brazil. Photographs of the main structures used in species identification, mainly from the male terminalia, are provided.