Phylogenomic pipelines discussion
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NameYour organism(s)Your data typeYour scientific questionPossible problemse-mailDiscussion group
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JannikDaphniaWhole genome dataReconstruct species relationship and date tree to look at environmental changes that might lead to speciation eventshybridizing species1
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JohanaCiliates (protists)transcriptomic and metagenomic data Relationships between main ciliate lineages, studying their modified mitochondria and its metabolism, their prokaryotic symbionts, finding mitochondrial 16S in the ciliatesjo.rotterova@gmail.com2
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CarolinaApicomplexa (Plasmodium, Haemoproteus, Lankesterella)single genePhylogenetic inference of new species, correlations with hosts, vectors and parasite specificity, zoogeographical distribution of different lineages2
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Abhijeet (AB)metagenomes,Bacteriatranscriptomic and metagenomic data Accurate taxonomic annotations in amplicon / whole genome metagenomic sequencing data and species inferenceIncorrect taxonomy in referecne databasesabhijeet.singh@slu.seYESAnaerobic Microbiology and Biotechnology, Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden3
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Jigyasa Arorametagenomes, gut bacteriametagenome datataxonomic annotation, ortholog detection,ancestral state reconstructionnot enough resolution in taxonomic analysis, orthologs etc, due to limitations of data in public databasesjigyasa-arora@oist.jpOkinawa Institute of Science and Technology Graduate University, Japan3
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Felipe SilvaPrimatesddRAD, Whole Genome SequencesReconstruct species relationshipHybridizarion, Incomplete Lineage Sortinginterfaceh@gmail.comYESUniversity of Salford5
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Nataly CanalesAngiosperms (Rubiaceae)(paleo)genomic and transcriptomic dataFind a phylogenetic signal in the alkaloid content. Correctly id adulterated collections. Trace historic commercialization of cinchona bark.Low amount and fragmented DNA + presence of exogenous DNA. Hybridization. Phylogeny not resolved yet.nataly.canales@snm.ku.dkyes!Natural History Museum of Denmark4
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Hamid GhanaviLepidoptera / InsectsFew whole genomes (50-100) combined with more (~2000) samples with few sanger sequence (~8 genes ~6000bp)Diversification dynamics (speciation/extinction rates)computationally heavy, incomplete datasetshamid.ghanavi@biol.lu.seOf course! :)Lund University1
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Isa SchonOstracods/ amphipodstranscriptomes & few genesreconstruct phylogenetic relationships, find potential hybridisation & HGT eventsnot enough data, distinguish HGT from contaminationischoen@naturalsciences.beYesRoyal Belgian Institute of Natural Sciences1
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Matej DolinayfrogsddRAD, Anchored hybrid enrichmentspecies delimitation and species tree inference using different methods, presence of gene flow in phylogenomic datadolinaym@gmail.comyes :)Institute of Vertebrate biology, Masaryk University5
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Emil HägglundPlanctomycetes (Bacteria)Whole genome data/MetagenomeIdentify adaptive gains and quantify the role of duplication/divergence, HGT and de novo origin.emil.hagglund@icm.uu.se3
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Marta Maria CiucaniWolf Whole genome - paleogenomics - paleoproteomicsReconstruct the relationships between ancient wolves and current wolves + dogs. Find events of hybridization between different canid species and between wolves and dogs.Low coverage5
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Arda GülayAmmonia oxidizing Bacteria and ArchaeaWhole genome data/Metagenomequantify and identify HGT and divergence events. ınferring evolutionary history of genes and aligning to geological timescalesHGT identificationardagulay@fas.harvard.eduyes :)Harvard University3
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Anna Seidlplantssingle gene and whole genome (population sampling)Relationship of populatins within species, dating, phylogeographic analysisGene flow between populations, only one fossil for dating analysis (so far)anna.seidl@boku.ac.atyesBOKU Vienna, Botany4
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Kaylee RichClade V nematodesWhole genome, proteomeHookworm phyogeny and evolution of hematophagy. Identification of vaccine/drug targets in hematophagous nematodesLack of data, whole genomes are missing for a lot of the nematodes that would help (only mitochondrial DNA or rDNA available), the worms of interest seem to be less related than originally thought (orthology-based methods aren't working as well as hoped)kaylee.rich@ucalgary.caYesUniversity of Calgary, Faculty of Vet Med1
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Laura Whitefleet-SmithOysters and single celled eukaryotic parasitesParasite-host coevolution, parasite strain phylogeography, Degraded DNA from preserved material (FFPE). Limited datalawhitef@vims.edu; lwhitefleetsmith@gmail.comYesVirginia Institute of Marine Science, Gloucester Point, VA, USA2
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MartinaChiroptera (bats), One ring species and its sympatric sister speciesWill be whole genomeTracing genomics changes in a ring species from the ancestral form to the two terminal formsnot sure yet 5
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Kumar Saurabh SinghAphids (Myzus persicae) High coverage population level genomic dataDating analysisClonal species, gene duplication, transposon insertionk.saurabh-singh@exeter.ac.ukUniversity of Exeter, Penryn Campus UK1
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Tijana
Dipterocarpaceae tropical tree family
the whole genome sequences
tree calibration and ancestral state reconstructionusing acurate fossils for tree calibration and their possitiontijana.cvetkovic@ymail.comGuangxi University, China4
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Alexander Bowles
Plants (Archaeplastida to angiosperms)
Whole genome/proteome
Understanding broad scale evolutionary patterns (e.g. kingdom/subkingdom-wide), Using comparative genomics to understand character and trait evolution
How to investigate trait evolution
AB17040@essex.ac.ukYesUniversity of Essex, UK4
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Ana PontesYeast (Saccharomyces cerevisiae)whole genomeunderstanding the different events of domestication and how they related with wild populationsap.pontes@fct.unl.ptFCT - New University of Lisbon2
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Raúl OrtizNon-conventional yeast / deep branching fungiwhole genome sequencing / transcriptomesTrait evolution, non-vertical evolutionpoliploidyraul.ortiz@tudelft.nlMaybeDelft University of Technology2
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Manuel BarriosWeevils!Genome/transcriptomesWhich are the variations in the genome to the life in soilLimited Data, horizontal gene transferencemanuelbarriosgt@gmail.comInstituto de Investigaciones de Zacapa5
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Jorge Eduardo Amaya RomeroAnopheles Mosquitoes, Heliconius butterfliesWhole genome sequencingIntrogression and hybridizationConfunding information in the genomej.e.amaya.romero@rug.nlYesUniversity of Groningen, Max PLanck, University of Montpellier5
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