Loftets stora Sal , Uppsala

Lunch Seminar "Molecular based ecological inventories - revisiting ecology”

By Dr. Alain Franc, INRA - UMR BioGeCo - Bordeaux, France.


Systematics and taxonomy are keystones for biodiversity studies, especially community ecology. Entering the scene with Linné, systematics and taxonomy have experienced three revolutions: first as becoming a branch of evolutionary biology, second with molecular biology, and recently, a third one with NGS (New Generation Sequencing). In this talk, I’ll present how tools have evolved recently due to NGS revolution, in order to derive community inventories from metagenomes of environmental samples. Time needed for inventory sampling is now much shorter than before, which permits to expand dramatically the number of available inventories. However, much work still remains before metabarcoding runs swiftly and accurately. Several tools exist to identify species from markers of taxonomic interest, some of which are over a decade old. However, most of them run on laptops, and some limitations on memory space or running time can be reached easily when working on NGS data. Second, those tools ideally require well curated data bases, which still is a demanding and not automatized task. I will present the example of NGS work on diatoms, an algal group often used for biomonitoring. Diatoms are unicellular eukaryotes which have been observed under microscope for several decades, and for which a huge expertise on morphologically based species identification exists. They are then ideal organisms for benchmark tests of molecular tools for automatic inventories. We present some results of comparisons between optical and molecular based inventories on diatoms communities, and sketch how increasing number of inventories repeated in space and time may shed light on community pattern.


Time: 2014-12-11 11:30 - 13:00
City: Uppsala
Location: Loftets stora Sal
Organiser: Focus on Soils and Water
Last signup date: 9 December 2014
Additional info:

Register for lunch (free of charge) by e-mail to Minh no later than 9th of December at 12:00. Please inform if you wish vegetarian food or have any food allergies/restrictions. Lunch is served at 11.30 at Loftets stora Sal  and the seminar starts at 12.00.


Minh Anh Nguyen, Charlotta Tiberg and Preetisri Baskaran.