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International audience; After causing mass disasters that claimed the lives of tens of thousands of soldiers from countries around the world, the two Great Wars left some of them lost and missing. In France, these corpses reside in a legal vagueness where they belong neither to forensic anthropology nor archeology. Nevertheless, the process of identification and determining the cause of death requires the use of modern forensic anthropology by applying biological profiling and DNA analysis. New genomic methods also provide insight into the health statuses of these military populations, providing new perspectives on these periods of humanitarian crisis.

Les épidémies font partie intégrante de l’Histoire des hommes. Elles les ont contraints à instaurer des mesures sociétales d’isolement afin de limiter la contagion. La maladrerie Saint-Lazare, implantée en périphérie de Beauvais, en est un exemple. Fondée au tournant des XIe-XIIe siècles, c’est une institution à double vocation, caritative et hospitalière, qui accueille alors des lépreux. Au XVIIe siècle, un nouvel espace est construit, hors de l’enceinte, mais proche du mur de clôture pour r...

International audience

An analysis of the distribution of surnames through time and space allows us to understand the structure of human groups, their exchanges or even their possible isolation. The French population has already been studied through surnames and it has been shown that the Sud-Provence-Alpes-Côte d’Azur region differed from the rest of France in both the 20th and 21st centuries (Mourrieras et al., 1995; Scapoli et al., 2005). The objective of this study was to understand the population evolution and particularities of the Sud-Provence-Alpes-Côte d’Azur region through an analysis of the distribution of surnames over an earlier period: the 19th century. For this work, 806,069 birth records from 521 communes between 1810 and 1890 were recorded and a total of 23,340 surnames were collected. The estimation of various isonymic parameters has allowed a description of this corpus never exploited before. In order to appreciate the population evolution, the data set was divided into three periods of 25 years. The canton was the geographical unit of this study, and similarities and differences between each of them were evaluated using Lasker distances, which allow the construction of dendrograms. A positive and significant correlation (pv-index of Karlin and McGregor (1967), showed higher values in the south-western quarter of the region. The decrease in Rst values across the three periods is consistent with a homogenization of the patronymic between the cantons. This three-period approach showed a population evolution influenced by linguistic, cultural, historical and migratory phenomena since the Middle Ages, disrupted by the socioeconomic changes of the 19th century.

International audience; Red cell blood group systems are crucial for safe transfusion, transplantation, and pregnancy monitoring. In addition, blood groups have long been investigated to decipher the origin of human populations, migration, adaptation, and admixture. However, since the extensive use of DNA polymorphisms in Anthropology, blood groups have been relegated to their primary application, blood transfusion. The finer genomic mapping of some Neanderthal and Denisova individuals about modern humans has provided significant evidence on the evolutionary history of both archaic and modern humans. However, despite their medical and anthropological interest, little is known about blood groups in archaic populations. To better understand the origin, expansion and encounter with Homo sapiens, we reappraised the available high-quality sequences of three Neanderthals (Vindija 33.19, Chagyrskaya 8, Altai Neandertal) and one Denisovan (Denisova 3) for 11 genes of the 7 blood group systems that are routinely screened in transfusion: ABO including H/ Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, and Diego. We show that Neanderthals and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing viral gut infection and all Neanderthal shared RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to possible pregnancies with complications. Lastly, we connect the Neanderthal RHD allele to two present-day Aboriginal Australians and Papuan, suggesting that a segment of the archaic genome was introgressed in this gene in non-Eurasian populations before their expansion towards Oceania. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems remain effective anthropological markers.

International audience; While recent advances in genetics make it possible to follow the genetic exchanges between populations and their phenotypic consequences, the impact of the genetic exchanges on the sensory perception of populations has yet to be explored. From this perspective, the present study investi- gated the consequences of African gene flow on odor perception in a Malagasy population with a predominantly East Asian genetic background. To this end, we combined psychophysical tests with genotype data of 235 individuals who were asked to smell the odorant molecule beta-ionone (βI). Results showed that in this population the ancestry of the OR5A1 gene significantly influences the ability to detect βI. At the individual level, African ancestry significantly protects against specific anosmia/hyposmia due to the higher frequency of the functional gene (OR ratios = 14, CI: 1.8–110, p-value = 0.012). At the population level, African introgression decreased the prevalence of specific anosmia/hyposmia to this odorous compound. Taken together, these findings validate the conjecture that in addition to cultural exchanges, genetic transfer may also influence the sensory perception of the population in contact.

Summary Background The remains of soldiers who died during the two World Wars are regularly discovered by chance or during land use planning . In an archaeological, anthropological and genetic analysis of these remains, it is important to provide the most exhaustive information possible on these discoveries in order to fulfill the duty of memory. The legal aspect is a central question when it comes to the place of these human remains . Methodology This article proposes a consideration of the situation from a legal point of view and suggests avenues of reflection for a complementary approach from several disciplines. Results/Discussion A focus on the term death for France have been proposed. This term is much more than a simple qualifier or a generic expression, it implies economic, patrimonial, but also moral consequences. It should be remembered that the dignity underlying such a status is likely to impact the meaning attached to the duty to remember. Conclusion More than anything else, we can see that the study of these contexts requires genuine interdisciplinary research in which the law is not invented but in which jurists and anthropologists have every opportunity to express themselves side by side.

We carried out a genome-wide association study in Latin Americans and identified novel face morphology loci.., To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.

International audience

SUMMARY The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

Cet article a été suscité à partir d’un double constat. Un constat factuel qui montre que lors de la Covid 19, de façon récurrente et sous des expressions diverses, les épidémies de peste ont été convoquées, à divers titres. Un constat anthropologique qui met en évidence non pas les similitudes historiques et épidémiologiques des crises épidémiques (Peste-Covid 19), ni une forme quelconque d’analogie possible, mais bien le dessin de la peste en filigrane de la Covid 19, au prisme de certains invariants anthropologiques : le rapport à la mort et son cortège de peurs, en temps de crise, liées à l’alimentation, à la contagion ; les rituels engendrés, de formes anciennes ou nouvelles ; les règles d’exception liées à la gestion de crise sanitaire. Il s’agit, par- delà les échos, les récurrences, de mettre à jour ces invariants structurant le social. This article was prompted by a twofold observation. A factual observation which shows that during the Covid 19, in a recurrent way and under various expressions, plague epidemics were summoned, for various reasons. An anthropological observation that highlights not the historical and epidemiological similarities of epidemic crises (Peste-Covid 19), nor any form of possible analogy, but rather the drawing of the plague as a watermark of Covid 19, through the prism of certain anthropological invariants : the rapport with death and its procession of fears, in times of crisis, linked to food and contagion ; the rituals generated, in old or new forms ; the rules of exception linked to the management of health crises. Beyond the echoes and recurrences, it is a question of updating these invariants of social structure.

This case study reports the anthropological analysis of bones remains discovered on Riou Island (Marseille, France) and the story of two World War II fighter pilots. The discovery of bones on “The Fountain of the Greeks” square on Riou Island occurred in the 1960’s and a first anthropological study described a 35-year-old man, about 1.77 m tall, buried since an estimated period between the 13th and 16th centuries. The case was “closed” and the bones were considered as isolated archaeological remains. Few years later, near the coasts of Riou Island, parts of two planes were discovered. One was from of a German Messerschmitt Bf 109 F-4 of the Luftwaffe piloted by Prince Alexis furst zu Bentheim und Steinfurt, and the other from a French P-38 Lightning F-5 B piloted by Antoine de Saint-Exupery. Therefore, the identification of the skeletal remains mentioned above was then thought to be perhaps one of the two World War II pilots. In this particular context we performed forensic and molecular biology analyses to resolve this identification.

International audience; The study of human remains from the first and the second World War is important for enhancing our understanding of that historical period. Despite the fact that the period has been well-documented previously, gaps remain, particularly as a result of the destruction of archives. In fact, for just WWI, more than 700,000 soldiers from both sides remain missing. Scientific and political collaborations established in hopes of recovering and identifying soldiers will allow many families understand “what happened” to their loved ones and facilitate the return of the soldiers their homes. In this paper, the recovery of the human remains of French soldiers WWI and WWII will be described through the lens of the legislation in place governing the retrieval and identification of the remains, protocols established for recovery, excavation and analysis, and the dissemination data. These features will be illustrated using three case studies that involve French soldiers who died during WWI. Research of this type is the result of true interdisciplinary and sometimes international, depending on the context, collaboration. The public and academic the dissemination of these archaeological discoveries, both to academics and the public, is crucial and a type of remembrance.

International audience

International audience; Étonnamment, l’histoire de l’« ADN ancien » (noté parfois ADNa) est une histoire qui a commencé il y a juste 35 ans. C’est en effet, en 1984, au balbutiement de la biologie moléculaire, qu’une équipe californienne (Higuchi et al., 1984) parvient à cloner un fragment d’ADN d’un quagga, une sous-espèce de zèbre éteinte à la fin du XIXe siècle. Cette découverte revenait à dénicher alors l’impensable : des reliquats « vivants » (organiques) dans du non-vivant. Par cette ressuscitation in vitro de l’information génétique ancienne, la communauté scientifique mesurait alors le nouveau potentiel de cette découverte.

Red cell polymorphisms can provide evidence of human migration and adaptation patterns. In Eurasia, the distribution of Diego blood group system polymorphisms remains unaddressed. To shed light on the dispersal of the Dia antigen, we performed analyses of correlations between the frequencies of DI*01 allele, C2-M217 and C2-M401 Y-chromosome haplotypes ascribed as being of Mongolian-origin and language affiliations, in 75 Eurasian populations including DI*01 frequency data from the HGDP-CEPH panel. We revealed that DI*01 reaches its highest frequency in Mongolia, Turkmenistan and Kyrgyzstan, expanding southward and westward across Asia with Altaic-speaking nomadic carriers of C2-M217, and even more precisely C2-M401, from their homeland presumably in Mongolia, between the third century BCE and the thirteenth century CE. The present study has highlighted the gene-culture co-migration with the demographic movements that occurred during the past two millennia in Central and East Asia. Additionally, this work contributes to a better understanding of the distribution of immunogenic erythrocyte polymorphisms with a view to improve transfusion safety.

Post-marital residence of spouses is one of the architects of population genetic structure. In the present study, we tested how the place of residence of males and females in Ngazidja, Comoros Islands, has unequally channeled, by dispersal among villages, the male and female genetic diversity. Using sequences of the hypervariable segment I of the mitochondrial DNA (mtDNA HVS-I) and six Y-chromosome microsatellites (Y-STRs), we measured the genetic variation and male-to-female effective number of migrants ratios based on FST values and revealed a genetic structure mostly driven by male gene flow across villages. This genetic feature illustrates the uxori-matrilocality inherited from the Bantu expansion, though one exception exists in Bandamadji whose historically documented military status implied patrilocality in this locality.

International audience; On islands, invasive predators, particularly feral cats and rats, are key drivers of bird population decline and extinction. Diet studies can be used to assess predator impacts on prey populations. Here we first evaluated the resolution of morphological identification (Class to Species) of bird remains in cat and rat diet studies. We also analysed the effect of predator size/type (cat vs rat) and sample type (faecal vs stomach contents) on the taxonomic level of bird identification. We found that difficulty in identifying bird remains significantly increased with taxonomic resolution (from Class to Species) for both predators. Bird identification was more accurate in cat than in rat diets and no sample-type effect was detected in cat diets. Second, we developed a set of molecular resources (DNA sequence database and bird-specific primer pairs) to detect and identify bird DNA. We tested and validated primer pairs' taxonomic coverage and specificity using in silico and in vitro analyses. The performances of morphological and molecular methods were then compared in a case study of cat and rat diet samples collected on Niau Atoll (French Polynesia). Our results highlight the efficiency of the molecular method in both detection and high-resolution identification of birds in predator diet samples. As robust qualitative and quantitative diet analyses are required to accurately assess predator impacts on prey populations, we recommend combining morphological and molecular methods to maximise bird detection, identification and quantification, especially when rare or threatened birds are at stake

Hybridization phenomena can be considered in different ways. Hybridization studies can be used to elucidate some aspects of speciation and adaptation. However, hybridization may be a threat to endemic species. Here, we studied bidirectional introgression between two sympatric species of Cyprinidae: Chondrostoma toxostoma toxostoma and C. nasus nasus. Analysis of morphology, allozymes and mtDNA sequences revealed that the hybridization between these two cyprinids takes different forms in the same river. The mosaic hybrid zone (so called because of the absence of a simple cline) appeared to be partitioned due to the proportions of the two species along a spatial scale. The proportion of each hybrid group in this zone was unstable over a 5-year period. We propose various protection/conservation states for the C. t. toxostoma populations based on the level of introgressive hybridization and the genetic structure of both species in ‘pure’ populations. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85, 135–155.

International audience; A total of 68 cyprinid microsatellites were screened for cross-species amplification in order to develop three PCR multiplex kits for the Eurasian minnow (Phoxinus phoxinus L.) and the gudgeon (Gobio gobio L.). The multiplex kits cluster 21 and 18 microsatellites for P. phoxinus and G. gobio, respectively. All loci were evaluated using ~80 individuals sampled from three distinct populations. By multiplexing the markers, we aim to decrease genotyping costs and increase time efficiency. These two microsatellite sets represent a valuable tool for ecological, evolutionary, conservation and management issues.

International audience; INTRODUCTION: Hybridization is a common phenomenon in fish and is considered to be a major source of diversification. Deciphering the remoulding of genomic regions and phenotypes in zones where hybrid specimens occur is of particular interest to elucidate the emergence of evolutionary novelties. This approach is particularly challenging because the first step of hybridization seems to be the most important stage in the emergence of hybrid lineages. However, the signal can be significantly altered after only a few generations. RESULTS: We studied 41 microsatellites and partial cytochrome b gene sequences in 970 specimens belonging to two fish species (Chondrostoma nasus and Parachondrostoma toxostoma) in allopatric/parapatric zones, hybrids between them in a natural sympatric zone: the Ardeche basin. We showed that the genomic architecture in hybrids presented pattern heterogeneity of selection for the different loci. Indeed, the upstream part of the river (Rosieres and Labeaume) presented an overdominant fitness of heterozygotes (12.20%) corresponding to a genomic compatibility, and underselection was observed for 4.88%-7.32% of the loci tested indicating a genomic incompatibility. Moreover the upstream station (Rosieres) presented a positive selection of invasive C. nasus homozygotes (17.07% to 21.95%) indicating that hybridization may increase the fitness of admixed individuals.We showed that hybrid morphology (body shape based on 21 landmarks) correlated with genomic dilution indicating a species fingerprint. However, we demonstrated that the hybrid morphology was not a linear modification between the two parental species but a trade-off between several correlated traits. CONCLUSIONS: Hybrid specimens present a mosaic of genomic combination, showing regions with genomic compatibility and others with genomic incompatibility between the two species. Positive selection (invasive advantage ranging from 9.76% to 21.95% of the loci) was evidenced in the upstream part of the Ardeche indicating that environmental selection makes a substantial contribution. Although the presence of a dam is known to impose heterogeneous hybrid zones between these two species, we demonstrated in this study that a natural environment can also generate a hybrid zone with a large number (and diversity) of hybrids. The combination of the two genomes in the hybrids results in complex ontogenetic trajectories (with different morphological traits evolving at different rates) that correspond to novel developmental pathways.

The development of DNA barcoding from faeces represents a promising method for animal diet analysis. However, current studies mainly rely on prior knowledge of prey diversity for a specific predator rather than on a range of its potential prey species. Considering that the feeding behaviour of teleosts may evolve with their environment, it could prove difficult to establish an exhaustive listing of their prey. In this article, we extend the DNA barcoding approach to diet analysis to allow the inclusion of a wide taxonomic range of potential prey items. Thirty-four ecological clade-specific primer sets were designed to cover a large proportion of prey species found in European river ecosystems. Selected primers sets were tested on isolated animal, algal or plant tissues and thereafter on fish faeces using nested PCR to increase DNA detection sensitivity. The PCR products were sequenced and analysed to confirm the identity of the taxa and to validate the method. The methodology developed here was applied to a diet analysis of three freshwater cyprinid species that are assumed to have similar feeding behaviour [Chondrostoma toxostoma toxostoma (Vallot 1837), Chondrostoma nasus nasus (Linnaeus, 1758) and Barbus barbus, (Linneaus 1758)]. These three species were sampled in four different hydrographic basins. Principal Component Analysis based on prey proportions identified distinct perilithon grazer and benthophagous behaviours. Furthermore, our results were consistent with the available literature on feeding behaviour in these fish. The simplicity of the PCR-based method and its potential generalization to other freshwater organisms may open new perspectives in food web ecology.

Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and next-generation sequencing on 454 GS-FLX Titanium platforms. The procedure was calibrated on a model species (Apis mellifera) and validated on 13 other species from various taxonomic groups (animals, plants and fungi), including taxa for which severe difficulties were previously encountered using traditional methods. We obtained from 11 497 to 34 483 sequences depending on the species and the number of detected microsatellite loci ranged from 199 to 5791. We thus demonstrated that this procedure can be readily and successfully applied to a large variety of taxonomic groups, at much lower cost than would have been possible with traditional protocols. This method is expected to speed up the acquisition of high-quality genetic markers for nonmodel organisms.

By combining biotin-enrichment protocol and next generation pyrosequencing, through 454 GS-FLX Titanium technology, 55 polymorphic microsatellites loci with perfect motif were isolated from the Rhone streber (Zingel asper), a critically endangered European fish species. Eight multiplex PCR kits were optimised in order to genotype a total of 58 polymorphic loci, including three previously published loci. The level of genetic diversity was assessed for 68 Z. asper, 30 Sander lucioperca, 33 Perca fluviatilis and four Gymnocephalus schraetzer individuals. Amplification success was also assessed on Romanichthys valsanicola and Zingel streber using single individuals. These markers will be useful to investigate the population structure of the highly fragmented Rhone streber. They represent a powerful tool for conservation issues and evolutionary approaches of this endemic species. Moreover, part of our markers demonstrated applicability to other percid species, allowing for potential applications to fisheries and aquaculture management.

Gilles, A., Costedoat, C., Barascud, B., Voisin, A., Banarescu, P., Bianco, P. G., Economidis, P. S., Maric, D. & Chappaz, R. (2010). Speciation pattern of Telestes souffia complex (Teleostei, Cyprinidae) in Europe using morphological and molecular markers.—Zoologica Scripta, 39, 225–242. It is notorious that many species boundaries are erroneously defined. When molecular markers are used, misleading evidence can notably be due to the characteristics inherent to mitochondrial DNA and quantity of markers used but also because of a limited range distribution sampling. European cyprinids biodiversity inventory is still an ongoing task and surprising phylogeographic patterns and phylogenetic relationships are still recovered on account of methodological evolution. This is particularly obvious for the Telestes souffia complex. This species occurs in a fragmented range and species boundaries is greatly debated. In this study, we provide an updated delimitation of the different evolutionary entities constituting this T. souffia complex and propose a taxonomic revision. Morphological and molecular analyses were carried out on 520 specimens coming from 19 localities representing the complete geographical range of this species complex and six related sister species that could potentially interact with it (outgroup ‘sensu lato’). Phylogenetic reconstructions and multivariate analyses demonstrated that the T. souffia complex is constituted of at least three species (T. souffia, Telestes muticellus and Telestes montenigrinus). Data also suggested that T. souffia comprises three subspecies (T. s. souffia, T. s. agassii; T. s. rysela). We also confirm the splitting of the T. souffia sister species Telestes pleurobipunctatus into two distinct species. The Peloponnesian lineage will be referred as Telestes alfiensis and the continental lineage as T. pleurobipunctatus. Morphological and molecular markers displayed some degree of incongruence within T. souffia suggesting that introgressive hybridization has played a role in the evolution of the Telestes genus. However, discordance among data sets could also result from heterogeneous rate of morphological evolution. Finally, we demonstrated that T. muticellus was implicated in two categories of hybridization: an inter-species hybridization (between T. muticellus and T. souffia) and an inter-generic hybridization (between T. muticellus and Squalius lucumonis), a phenomenon rarely observed for a same species.

Background Cyprinids display the most abundant and widespread species among the European freshwater Teleostei and are known to hybridize quite commonly. Nevertheless, a limited number of markers for conducting comparative differentiation, evolutionary and hybridization dynamics studies are available to date. Findings Five multiplex PCR sets were optimized in order to assay 41 cyprinid-specific polymorphic microsatellite loci (including 10 novel loci isolated from Chondrostoma nasus nasus, Chondrostoma toxostoma toxostoma and Leuciscus leuciscus) for 503 individuals (440 purebred specimens and 63 hybrids) from 15 European cyprinid species. The level of genetic diversity was assessed in Alburnus alburnus, Alburnoides bipunctatus, C. genei, C. n. nasus, C. soetta, C. t. toxostoma, L. idus, L. leuciscus, Pachychilon pictum, Rutilus rutilus, Squalius cephalus and Telestes souffia. The applicability of the markers was also tested on Abramis brama, Blicca bjoerkna and Scardinius erythrophtalmus specimens. Overall, between 24 and 37 of these markers revealed polymorphic for the investigated species and 23 markers amplified for all the 15 European cyprinid species. Conclusions The developed set of markers demonstrated its performance in discriminating European cyprinid species. Furthermore, it allowed detecting and characterizing hybrid individuals. These microsatellites will therefore be useful to perform comparative evolutionary and population genetics studies dealing with European cyprinids, what is of particular interest in conservation issues and constitutes a tool of choice to conduct hybridization studies.

Background Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The acquisition of microsatellites through multiplex-enriched libraries and 454 GS-FLX Titanium pyrosequencing is a promising new tool for the isolation of new markers in unknown genomes. This approach can also be used to evaluate the extent to which microsatellite-enriched libraries are representative of the genome from which they were isolated. In this study, we deciphered potential discrepancies in microsatellite content recovery for two reference genomes (Apis mellifera and Danio rerio), selected on the basis of their extreme heterogeneity in terms of the proportions and distributions of microsatellites on chromosomes. Results The A. mellifera genome, in particular, was found to be highly heterogeneous, due to extremely high rates of recombination, with hotspots, but the only bias consistently introduced into pyrosequenced multiplex-enriched libraries concerned sequence length, with the overrepresentation of sequences 160 to 320 bp in length. Other deviations from expected proportions or distributions of motifs on chromosomes were observed, but the significance and intensity of these deviations was mostly limited. Furthermore, no consistent adverse competition between multiplexed probes was observed during the motif enrichment phase. Conclusions This approach therefore appears to be a promising strategy for improving the development of microsatellites, as it introduces no major bias in terms of the proportions and distribution of microsatellites.

Summary: QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input. The following tasks are completed by QDD: tag sorting, adapter/vector removal, elimination of redundant sequences, detection of possible genomic multicopies (duplicated loci or transposable elements), stringent selection of target microsatellites and customizable primer design. It can treat up to one million sequences of a few hundred base pairs in the tag-sorting step, and up to 50 000 sequences in a single input file for the steps involving estimation of sequence similarity. Availability: QDD is freely available under the GPL licence for Windows and Linux from the following web site: http://www.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html Contact: emese.meglecz@univ-provence.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Background The invasive Chondrostoma nasus nasus has colonized part of the distribution area of the protected endemic species Chondrostoma toxostoma toxostoma. This hybrid zone is a complex system where multiple effects such as inter-species competition, bi-directional introgression, strong environmental pressure and so on are combined. Why do sympatric Chondrostoma fish present a unidirectional change in body shape? Is this the result of inter-species interactions and/or a response to environmental effects or the result of trade-offs? Studies focusing on the understanding of a trade-off between multiple parameters are still rare. Although this has previously been done for Cichlid species flock and for Darwin finches, where mouth or beak morphology were coupled to diet and genetic identification, no similar studies have been done for a fish hybrid zone in a river. We tested the correlation between morphology (body and mouth morphology), diet (stable carbon and nitrogen isotopes) and genomic combinations in different allopatric and sympatric populations for a global data set of 1330 specimens. To separate the species interaction effect from the environmental effect in sympatry, we distinguished two data sets: the first one was obtained from a highly regulated part of the river and the second was obtained from specimens coming from the less regulated part. Results The distribution of the hybrid combinations was different in the two part of the sympatric zone, whereas all the specimens presented similar overall changes in body shape and in mouth morphology. Sympatric specimens were also characterized by a larger diet behavior variance than reference populations, characteristic of an opportunistic diet. No correlation was established between the body shape (or mouth deformation) and the stable isotope signature. Conclusion The Durance River is an untamed Mediterranean river despite the presence of numerous dams that split the river from upstream to downstream. The sympatric effect on morphology and the large diet behavior range can be explained by a tendency toward an opportunistic behavior of the sympatric specimens. Indeed, the similar response of the two species and their hybrids implied an adaptation that could be defined as an alternative trade-off that underline the importance of epigenetics mechanisms for potential success in a novel environment.

International audience; The phylogeographic studies of unrelated species that share overlapping distributions lead to new perspectives. Indeed, if different species with similar distributions shared the same phylogeographic pattern, then a common extrinsic cause could be proposed, involving some important issues for species conservation. Considering different mitochondrial studies of European freshwater fishes (threatened or not), it will be possible to perform such a comparative phylogeographic analyses. However, we illustrated how similar mitochondrial patterns can be due to different demographic models or evolutionary scenarios inducing numerous pitfalls. In this review, we present some major theoretical and practical challenges on phylogeography that need to be overcome before the inference of a global scenario. More than the evolution of the phylogeography discipline, estimation of the history of populations/species and their relationships is one of the most important challenges for conservation managers.

International audience; Ten novel polymorphic microsatellites were isolated from the dace complex (Leuciscus leuciscus), which is a European cyprinid species. Four multiplex polymerase chain reaction sets were optimized in order to genotype 26 polymorphic loci in all, including 16 previously published cyprinid-specific loci. The level of genetic diversity was assessed in 142 dace individuals. We also successfully applied 26 of the microsatellites to 10 related species. These primers thus will be useful to assess population structure of the dace and other cyprinid species, with application for conservation issues and phylogeographical approaches.