Biomedical subjects

François Pompanon

Publications and source records attributed to François Pompanon.

5 recordsLinked to original sources

PubMed2006

Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding.

DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254-767 bp) and of a shorter fragment of this intron (the P6 loop, 10-143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.

Base Sequence↗

PubMed2006

Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria).

Today, with the rapid development of population genomics, the genetic basis of adaptation can be unraveled directly at the genome level, without any prerequisites about the selectively advantageous genes or traits. For nonmodel species, it is now possible to screen many markers randomly scattered across the genome and to distinguish between the neutral genetic background and outlier loci displaying an atypical behavior (e.g., a higher differentiation between populations). This study investigated the genetic frame of adaptation to a gradient of altitude in the common frog (Rana temporaria) by means of a genome scan based on 392 amplified fragment length polymorphism markers. Using two outlier detection methods never applied to dominant data so far, we sought for loci with a genetic differentiation diverging from neutral expectations when comparing populations from different altitudes. All the detected loci were sorted out according to their most probable cause for outlier behavior and classified as false positives, outliers due to local effects, or outliers associated with altitude. Altogether, eight good candidate loci were identified as potentially involved in adaptation to altitude because they were picked out in several independent interaltitude comparisons. This result illustrated the potential of genome-wide surveys to reveal selection signatures along selection gradients, where the association between environmental variables and fitness-related traits may be complex and/or cryptic. In this article, we also underlined the need for confirmation of the selection footprints for the outlier loci. Finally, we provided some preliminary insights into the genetic basis of adaptation along an altitudinal cline in the common frog.

Adaptation, Physiological↗

PubMed2005

Use of amplified fragment length polymorphism (AFLP) markers in surveys of vertebrate diversity.

The amplified fragment length polymorphism (AFLP) technique is one of the most informative and cost-effective fingerprinting methods. It produces polymerase chain reaction (PCR)-based multi-locus genotypes helpful in many areas of population genetics. This chapter focuses on technical laboratory information to successfully develop the AFLP technique for vertebrates. Several AFLP protocols are described, as well as recommendations about important factors of the procedure such as the choice of enzyme and primer combinations, the choice and scoring of markers, the influence of the genome size on the AFLP procedure, and the control and estimation of genotyping errors. Finally, this chapter proposes a troubleshooting guide to help resolve the main technical difficulties encountered during the AFLP procedure.

Animals↗

PubMed2005

Genotyping errors: causes, consequences and solutions.

Although genotyping errors affect most data and can markedly influence the biological conclusions of a study, they are too often neglected. Errors have various causes, but their occurrence and effect can be limited by considering these causes in the production and analysis of the data. Procedures that have been developed for dealing with errors in linkage studies, forensic analyses and non-invasive genotyping should be applied more broadly to any genetic study. We propose a protocol for estimating error rates and recommend that these measures be systemically reported to attest the reliability of published genotyping studies.

Animals↗

PubMed2002

Speciation in the globeflower fly Chiastocheta spp. (Diptera: Anthomyiidae) in relation to host plant species, biogeography, and morphology.

Phylogenetic relationships among the Chiastocheta species (Diptera, Anthomyiidae) were investigated using a 1320-bp mitochondrial DNA fragment including parts of cytochrome oxidase subunits I and II. Larvae of the Chiastocheta genus feed exclusively on Trollius (Ranunculaceae) seeds. Six Chiastocheta species (and two vicariant taxa) coexist on Trollius europaeus in Europe, where they were shown to be the sole pollinator of their host plant. In Asia, several Trollius species are parasitized by Chiastocheta spp., and several other Trollius species are free of Chiastocheta. The plant-insect association is thus obligate in Europe but facultative in Asia. This system therefore provides a unique opportunity to study the evolution of an obligate mutualism between a plant and its seed parasite pollinators and its consequences on insect diversification. Most parsimonious, distance, and maximum likelihood analyses of 16 haplotypes from Europe and 14 from Asia show that European species do not form a monophyletic group. The species relationship indicated by egg morphology is only partly supported by molecular data. Moreover, a strong discrepancy between nucleotide variation and male genitalia morphology variation was found, particularly within and among European species coexisting on a single host plant. Molecular divergence across species ranges from 0 to 4.6%, suggesting a recent origin of the genus and several events of diversification, involving both host shifts and within-host-plant radiation. We discuss alternative evolutionary scenarios that are consistent with molecular data.

Animals↗