Emmanuelle Baudry

DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae)

In DNA barcoding, a short standardized DNA sequence is used to assign unknown individuals to species and aid in the discovery of new species. A fragment of the mitochondrial gene cytochrome c oxidase subunit 1 is emerging as the standard barcode region for animals. However, patterns of mitochondrial variability can be confounded by the spread of maternally transmitted bacteria that cosegregate with mitochondria. Here, we investigated the performance of barcoding in a sample comprising 12 species of the blow fly genus Protocalliphora, known to be infected with the endosymbiotic bacteria Wolbachia. We found that the barcoding approach showed very limited success: assignment of unknown individuals to species is impossible for 60% of the species, while using the technique to identify new species would underestimate the species number in the genus by 75%. This very low success of the barcoding approach is due to the non-monophyly of many of the species at the mitochondrial level. We even observed individuals from four different species with identical barcodes, which is, to our knowledge, the most extensive case of mtDNA haplotype sharing yet described. The pattern of Wolbachia infection strongly suggests that the lack of within-species monophyly results from introgressive hybridization associated with Wolbachia infection. Given that Wolbachia is known to infect between 15 and 75% of insect species, we conclude that identification at the species level based on mitochondrial sequence might not be possible for many insects. However, given that Wolbachia-associated mtDNA introgression is probably limited to very closely related species, identification at the genus level should remain possible.

Molecular identification of symbiotic dinoflagellates in Pacific corals in the genus Pocillopora

The authors regret that they made an error in reporting the primers used to amplify and sequence the ITS1 region, mentioned in the Material and methods section. The primer ITSint-rev was incorrectly reported and an internal primer which was incorrectly omitted has been added below. Materials and methods PCR amplifications of zooxanthellae nrDNA [The second paragraph of this section should be replaced with the following text] To investigate zooxanthella diversity in more detail, the Internal Transcribed Spacer 1 region (ITS1), which is a non-coding region that evolves faster than the 28S nrDNA (Santos et al. 2002a), was sequenced. Two primers were used to amplify both ITS1 and ITS2: one designed in the 3 0-end of the 18S DNA [ITS-for: 5 0-CGG TGA ATT ATT CGG ACT GAC-3 0 ; reverse of SYM3, modified from Hunter et al. (1997)] and the other in the 5 0-end of the 28S DNA [ITS-rev: 5 0-TCC TCC GCT TAT TGA TAT GC-3 0 from Hunter et al. (1997)]. The PCR protocol was identical to that of 28S nrDNA amplification, except amplifications were carried out in a total volume of 30 ll. Amplified products were purified using QIAquick PCR purification kit (Qiagen) following the manufacturers instructions and ITS1 region was directly sequenced in both directions using 3.2 pmol of the primer ITS-for and an internal primer in the 5.8S region [ITSint-rev: 5 0-CAC GGA GTT CTG CAA TTC-3 0 (reverse of ITSintfor2 from LaJeunesse and Trench (2000))]. [The region ITS2 can be sequenced using ITS-rev and ITSintfor2 from LaJeunesse and Trench (2000).] Reagents and cycling conditions were as specified in the ABI Prism Big Dye Terminator Cycle Sequencing Ready Reaction kit (PE Applied Biosystems, Foster City, California).

Factors affecting male and female reproductive success in a chipmunk (Tamias sibiricus) with a scramble competition mating system

While sexual selection in mammals with female defense systems has historically received considerable attention, much less is known about the factors affecting reproductive success in mammalian species with scramble competition mating systems. Using mark–recapture techniques and DNA microsatellite loci to assign parentage, we examined the mating system and factors affecting the variation of the annual reproductive success in an introduced population of the Siberian chipmunk, Tamias sibiricus, a small, monomorphic, solitary squirrel. Our analyses showed that breeding females were spatially dispersed, setting the stage for a scramble competition mating system. Male reproductive success was positively associated with the size of the home range. The strength of sexual selection on this behavioral trait was very strong, equaling previous estimates for morphological traits in female defense mating systems. These findings suggest that a behavioral trait, space use, strongly influences the annual reproductive success in males, which is consistent with expectations in a scramble competition mating system. In both sexes, reproductive success was influenced by habitat, with twice as many juveniles produced in semi-open than in closed habitat, possibly due to differences in food availability between the two habitats.

A viable population of the European red squirrel in an urban park.

Whether urban parks can maintain viable and self-sustaining populations over the long term is questionable. In highly urbanized landscapes, urban parks could play a role in biodiversity conservation by providing habitat and resources to native species. However, populations inhabiting urban parks are usually small and isolated, leading to increased demographic stochasticity and genetic drift, with expected negative consequences on their viability. Here, we investigated a European red squirrel population located in an urban park close to Paris, France (Parc de Sceaux; 184 ha) to assess its viability. Using mitochondrial D-loop sequences and 13 microsatellite loci, we showed that the population presented high levels of genetic variation and no evidence of inbreeding. The size of the population was estimated at 100–120 individuals based on the comparison of two census techniques, Distance Sampling and Capture-Mark-Recapture. The estimated heterozygosity level and population size were integrated in a Population Viability Analysis to project the likelihood of the populations persistence over time. Results indicate that the red squirrel population of this urban park can be viable on the long term (i.e. 20 years) for a range of realistic demographic parameters (juvenile survival at least >40%) and immigration rates (at least one immigration event every two years). This study highlights that urban parks can be potential suitable refuges for the red squirrel, a locally threatened species across western European countries, provided that ecological corridors are maintained.

The Jewel Wasp – Nasonia

The genus Nasonia belongs to a large and diverse group of insects the parasitoid wasps. Adult parasitoid wasps are free-living and lay their eggs in or on various life stages of arthropods (e.g., insects, ticks, mites). Parasitoids include more species beneficial to humans than any other insect group. Since parasitoid Hymenoptera are known to attack significant vectors of human diseases, such as house flies, roaches, and ticks, and pests of agricultural importance, they received great attention from areas such as applied entomology and integrated pest management. They are also important regulators of agricultural pests and as such have a major impact on human food resources. Their impact on humans by reducing the destruction of agricultural products is indeed staggering. In the USA alone, biological control programs using parasitoid wasps allows saving on approximately

The geographic scale of genetic differentiation in the feral pigeon (Columba livia): implications for management

20 billion dollars annually by reducing crop loss caused by new invasive species; this number does not include the vast savings from biological control of native pests. Human health benefits directly from parasitoid Hymenoptera, since the group’s ability to regulate native and invasive pest species helps in reducing the application of pesticides that are potentially harmful to human health. The genus Nasonia has become a model system to study the genetic architecture of phenotypic traits important both for basic and applied biology

Genetic structure of the French red squirrel populations: implication for conservation.

Understanding the genetic connectivity among populations of spreading and problematic species is important to determine the spatial scale at which management actions need to be conducted. The feral pigeon (Columba livia) is considered to be a pest or an invasive species in many cities around the world, leading to frequent attempts to control its populations. In the present study, we used microsatellites markers to investigate the relationship between genetic structure and geographic distance among feral pigeons from different locations, and the patterns of genetic differentiation at two geographic scales, within and between urbanised areas. A Mantel’s test revealed that the levels of genetic differentiation increased significantly with the geographic distance separating the locations. We also found that neighbouring locations within urban areas are usually not genetically differentiated, suggesting that all of the feral pigeons in an urban zone constitute a single management unit. Our results suggest that in large, interconnected cities control by culling at the scale of a neighbourhood, in addition of generating ethical issues, will not be effective to decrease pigeon population sizes.

The righting response as a fitness index in freshwater turtles

The decline of the red squirrel (Sciurus vulgaris) in several European countries due to the introduction of the American grey squirrel (S. carolinensis) and the predicted arrival of the grey squirrel in France in the near future has lead to the development of a preventative conservation project in this country. In this study, we conducted an extensive survey of mitochondrial DNA variation in French red squirrels using a fragment of the mitochondrial D-loop and we compared the results with previously published data from other European populations. Our main aims were: (1) to determine whether genetically differentiated populations, which could represent prioritized units for conservation purposes, were present in France and (2) to determine whether the French population, which is currently largely undisturbed, could provide information on the postglacial recolonization history of the species. We found that French D-loop haplotypes show almost no tendency to cluster by geographic origin, be it region or country, suggesting that French red squirrels have not been isolated from other populations during an evolutionarily significant period and that they do not constitute an Evolutionary Significant Unit. The French red squirrels showed strong signals of population expansion, the opposite to what is observed in most other European populations, making them of particular interest to study the postglacial expansion history of the species.