Phylogenomic pipelines discussion

	A	B	C	D	E	F	G	H	I
1	Name	Your organism(s)	Your data type	Your scientific question	Possible problems	e-mail			Discussion group

2	Jannik	Daphnia	Whole genome data	Reconstruct species relationship and date tree to look at environmental changes that might lead to speciation events	hybridizing species				1
3	Johana	Ciliates (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 ciliates		jo.rotterova@gmail.com			2
4	Carolina	Apicomplexa (Plasmodium, Haemoproteus, Lankesterella)	single gene	Phylogenetic inference of new species, correlations with hosts, vectors and parasite specificity, zoogeographical distribution of different lineages					2
5	Abhijeet (AB)	metagenomes,Bacteria	transcriptomic and metagenomic data	Accurate taxonomic annotations in amplicon / whole genome metagenomic sequencing data and species inference	Incorrect taxonomy in referecne databases	abhijeet.singh@slu.se	YES	Anaerobic Microbiology and Biotechnology, Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden	3
6	Jigyasa Arora	metagenomes, gut bacteria	metagenome data	taxonomic annotation, ortholog detection,ancestral state reconstruction	not enough resolution in taxonomic analysis, orthologs etc, due to limitations of data in public databases	jigyasa-arora@oist.jp		Okinawa Institute of Science and Technology Graduate University, Japan	3
7	Felipe Silva	Primates	ddRAD, Whole Genome Sequences	Reconstruct species relationship	Hybridizarion, Incomplete Lineage Sorting	interfaceh@gmail.com	YES	University of Salford	5
8	Nataly Canales	Angiosperms (Rubiaceae)	(paleo)genomic and transcriptomic data	Find 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.dk	yes!	Natural History Museum of Denmark	4
9	Hamid Ghanavi	Lepidoptera / Insects	Few whole genomes (50-100) combined with more (~2000) samples with few sanger sequence (~8 genes ~6000bp)	Diversification dynamics (speciation/extinction rates)	computationally heavy, incomplete datasets	hamid.ghanavi@biol.lu.se	Of course! :)	Lund University	1
10	Isa Schon	Ostracods/ amphipods	transcriptomes & few genes	reconstruct phylogenetic relationships, find potential hybridisation & HGT events	not enough data, distinguish HGT from contamination	ischoen@naturalsciences.be	Yes	Royal Belgian Institute of Natural Sciences	1
11	Matej Dolinay	frogs	ddRAD, Anchored hybrid enrichment	species delimitation and species tree inference using different methods, presence of gene flow in phylogenomic data		dolinaym@gmail.com	yes :)	Institute of Vertebrate biology, Masaryk University	5
12	Emil Hägglund	Planctomycetes (Bacteria)	Whole genome data/Metagenome	Identify adaptive gains and quantify the role of duplication/divergence, HGT and de novo origin.		emil.hagglund@icm.uu.se			3
13	Marta Maria Ciucani	Wolf	Whole genome - paleogenomics - paleoproteomics	Reconstruct the relationships between ancient wolves and current wolves + dogs. Find events of hybridization between different canid species and between wolves and dogs.	Low coverage				5
14	Arda Gülay	Ammonia oxidizing Bacteria and Archaea	Whole genome data/Metagenome	quantify and identify HGT and divergence events. ınferring evolutionary history of genes and aligning to geological timescales	HGT identification	ardagulay@fas.harvard.edu	yes :)	Harvard University	3
15	Anna Seidl	plants	single gene and whole genome (population sampling)	Relationship of populatins within species, dating, phylogeographic analysis	Gene flow between populations, only one fossil for dating analysis (so far)	anna.seidl@boku.ac.at	yes	BOKU Vienna, Botany	4
16	Kaylee Rich	Clade V nematodes	Whole genome, proteome	Hookworm phyogeny and evolution of hematophagy. Identification of vaccine/drug targets in hematophagous nematodes	Lack 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.ca	Yes	University of Calgary, Faculty of Vet Med	1
17	Laura Whitefleet-Smith	Oysters and single celled eukaryotic parasites		Parasite-host coevolution, parasite strain phylogeography,	Degraded DNA from preserved material (FFPE). Limited data	lawhitef@vims.edu; lwhitefleetsmith@gmail.com	Yes	Virginia Institute of Marine Science, Gloucester Point, VA, USA	2
18	Martina	Chiroptera (bats), One ring species and its sympatric sister species	Will be whole genome	Tracing genomics changes in a ring species from the ancestral form to the two terminal forms	not sure yet				5
19	Kumar Saurabh Singh	Aphids (Myzus persicae)	High coverage population level genomic data	Dating analysis	Clonal species, gene duplication, transposon insertion	k.saurabh-singh@exeter.ac.uk		University of Exeter, Penryn Campus UK	1
20	Tijana	Dipterocarpaceae tropical tree family	the whole genome sequences	tree calibration and ancestral state reconstruction	using acurate fossils for tree calibration and their possition	tijana.cvetkovic@ymail.com		Guangxi University, China	4
21	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.uk	Yes	University of Essex, UK	4
22	Ana Pontes	Yeast (Saccharomyces cerevisiae)	whole genome	understanding the different events of domestication and how they related with wild populations		ap.pontes@fct.unl.pt		FCT - New University of Lisbon	2
23	Raúl Ortiz	Non-conventional yeast / deep branching fungi	whole genome sequencing / transcriptomes	Trait evolution, non-vertical evolution	poliploidy	raul.ortiz@tudelft.nl	Maybe	Delft University of Technology	2
24	Manuel Barrios	Weevils!	Genome/transcriptomes	Which are the variations in the genome to the life in soil	Limited Data, horizontal gene transference	manuelbarriosgt@gmail.com		Instituto de Investigaciones de Zacapa	5
25	Jorge Eduardo Amaya Romero	Anopheles Mosquitoes, Heliconius butterflies	Whole genome sequencing	Introgression and hybridization	Confunding information in the genome	j.e.amaya.romero@rug.nl	Yes	University of Groningen, Max PLanck, University of Montpellier	5
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