Evolutionary and Environmental Genomics @Hull evohull.org/environmental-genomics Dr Dave Lunt [email protected] 10th December 2013

Evolutionary and Environmental Genomics @Hull Research Areas Dr Africa Gómez Dr Bernd Hänfling Dr Domino Joyce Dr Darren Evans Dr Dave Lunt Dr Lori Lawson Handley Bioinformatics, Next Gen sequencing, DNA metabarcoding, phylogenomics, Ecological networks, conservation biology Invasive species, population genetics, phylogeography, conservation biology Speciation, adaptive radiations, hybridisation, behavioural biology Invasive species, ladybirds, dispersal and colonisation Phylogeography, dispersal and gene flow, cryptic species, sexual systems

Evolutionary and Environmental Genomics @Hull Facilities Facilities for Evolutionary and Environmental Genomics • Molecular genetics laboratories • Ancient DNA facility • Bioinformatics laboratory • Sample preparation and archiving facility • Excellent microscopy labs • Tropical and temperate aquaria • Growth rooms

Evolutionary and Environmental Genomics @Hull Ancient DNA Species identification, population structure, taxonomy • Specialist clean-room ancient DNA facility • Museum specimens • Sub-fossil remains • DNA extraction from formalin preserved specimens

Evolutionary and Environmental Genomics @Hull Invasive Species Next generation approaches to detection, identification and monitoring • Environmental DNA • Metabarcoding of massively pooled samples • Diagnostic probes Dr Africa Gómez Dr Bernd Hänfling Dr Darren Evans Dr Lori Lawson Handley

Evolutionary and Environmental Genomics @Hull Invasive Species Population genomics of crucian carp • Are crucian carp native or introduced? • To what extent are they hybridising with native carp? • Can next-generation genome sequencing identify genes of adaptive significance? RADseq and genomics bioinformatics Dr Bernd Hänfling

Evolutionary and Environmental Genomics @Hull Agricultural Evolutionary Genomics Comparative genomics of root knot nematodes • Cause 5% loss in world agriculture/ yr • Hybrid origins of major pathogenic species • How does genome content reflect plant parasitic range? Dr Dave Lunt Comparative genomics of 20 species underway Identification of origins Investigation of genomic basis of parasitism

Evolutionary and Environmental Genomics @Hull DNA barcoding Species identification, biodiversity and population structure

Evolutionary and Environmental Genomics @Hull DNA metabarcoding Mesofauna of organic and conventional farm soils • What mesofaunal species are typical in UK farm soils? • Are soil communities affected by farming method? • Over what scale does variation occur? Dr Darren Evans Dr Dave Lunt Dr Lori Lawson Handley

Evolutionary and Environmental Genomics @Hull DNA metabarcoding Mesofauna of organic and conventional farm soils • Collembola and nematodes are hyper- diverse • Approximately 500 species per 500cm3 soil • Micro-heterogeneity: every sample is different! Dr Darren Evans Dr Lori Lawson Handley Dr Dave Lunt

Evolutionary and Environmental Genomics @Hull Bioinformatics Metabarcoding, genome diversity, adaptive evolution, population genomics • Bioinformatics laboratory • Computational grid • Group bioinformatician • Undergraduate courses • Phylogenomics Bioinformatics is likely to be the limiting resource for Environmental Genomics

Evolutionary and Environmental Genomics @Hull evohull.org/environmental-genomics Dr Dave Lunt [email protected] 10th December 2013