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Integrating Fossils and Recent Taxa in the Study of Rove Beetle Evolution and Systematics Janina L Kypke

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Integrating Fossils and Recent Taxa in the Study of Rove Beetle Evolution and Systematics Janina L Kypke Integrating fossils and recent taxa in the study of rove beetle evolution and systematics Janina L Kypke Supervisors Dr. Alexey Solodovnikov Prof. Dr. Fredrik Ronquist Why study Staphylinidae? Ubiquitous • Largest animal family ! >60.000 species • 32 subfamilies à Short elytra à Flexible abdomen Why study Staphylinidae? Ubiquitous • Largest animal family ! >60.000 species • 32 subfamilies Why study Staphylinidae? • Largest animal family ! >60.000 species • 32 subfamilies Main PhD goals Main PhD goals Main PhD goals me Main PhD goals me Main PhD goals me Main PhD goals me Morphological data Molecular data Morphological data Molecular data Scydmaenidae Oxytelinae Silphidae PiesBnae Glypholomanae Osoriinae 1 PiesBnae Empelinae Omaliinae Megalopsidiinae Omaliine Habrocerinae Microsilphinae Group Trigunoridae Proteininae Trichophyinae Micropeplinae • conflicng Phloeocharinae 1 Neophoninae Scaphidiinae Dasycerinae • parBally unresolved ApateBcinae Protopselaphinae Omaliinae Pselaphinae Empelinae Tachyporine Tachyporinae pars Glypholomanae Microsilphinae Group Phoeocharinae Proteininae Olisthaerinae Staphylininae Tachyporinae pars Paederinae Trichophyinae Olisthaerinae Habrocerinae Tachyporinae 1 Aleocharinae Pseudopsinae Oxyteline Trigonurinae Micropeplinae Group ApateBcinae Pselaphinae Scaphidiinae Dasycerinae PiesBnae Neophoninae Osoriinae Osoriinae 2 Oxytelinae Phloeocharinae 2 Oxyporinae Aleocharinae Staphylinine Megalopsidiinae Scydmaeninae Group Steninae Solierinae EuaestheBnae EuaestheBnae Solieriinae Steninae Leptotyphlinae Oxyporinae Pseudopsinae Leptotyphlinae Staphylininae Tachyporinae 2 Thayer 2005 Paederinae Silphidae aer McKenna et al. 2014 Morphological data Molecular data Scydmaenidae Oxytelinae Silphidae PiesBnae Glypholomanae Osoriinae 1 PiesBnae Empelinae Omaliinae Megalopsidiinae Omaliine Habrocerinae Microsilphinae Group Trigunoridae Proteininae Trichophyinae Micropeplinae • conflicng Phloeocharinae 1 Neophoninae Scaphidiinae Dasycerinae • parBally unresolved ApateBcinae Protopselaphinae Omaliinae Pselaphinae Empelinae Tachyporine Tachyporinae pars Glypholomanae Microsilphinae Group Phoeocharinae Proteininae Olisthaerinae • homology vs. homoplasy Staphylininae Tachyporinae pars • sample size too small Paederinae Trichophyinae • not enough data Olisthaerinae Habrocerinae Tachyporinae 1 Aleocharinae • no fossils included Pseudopsinae Oxyteline Trigonurinae Micropeplinae Group ApateBcinae Pselaphinae Scaphidiinae Dasycerinae PiesBnae Neophoninae Osoriinae Osoriinae 2 Oxytelinae Phloeocharinae 2 Oxyporinae Aleocharinae Staphylinine Megalopsidiinae Scydmaeninae Group Steninae Solierinae EuaestheBnae EuaestheBnae Solieriinae Steninae Leptotyphlinae Oxyporinae Pseudopsinae Leptotyphlinae Staphylininae Tachyporinae 2 Thayer 2005 Paederinae Silphidae aer McKenna et al. 2014 WorkGlow – Target Capture lyse bind wash elute WorkGlow – Target Capture Transcriptome assembly single reads - exons lyse bind wash elute transcriptome WorkGlow – Target Capture Transcriptome assembly single reads - exons IdenBficaon of single copy & lyse bind wash elute orthologous loci transcriptome © T. & D. Pendleton Nicrophorus vespilloides ref. genome single copy genes WorkGlow – Target Capture Transcriptome assembly single reads - exons IdenBficaon of single copy & lyse bind wash elute orthologous loci Transcriptome alignment transcriptome © T. & D. Pendleton Nicrophorus vespilloides ref. genome transcriptomes single copy genes 1 2 3 WorkGlow – Target Capture Transcriptome assembly single reads - exons IdenBficaon of single copy & lyse bind wash elute orthologous loci Transcriptome alignment transcriptome Reference genome comparison © T. & D. Pendleton introns Nicrophorus vespilloides ref. genome transcriptomes single copy genes 1 2 3 WorkGlow – Target Capture Transcriptome assembly IdenBficaon of single copy & lyse bind wash elute orthologous loci probes single copy genes Transcriptome alignment Reference genome comparison © T. & D. Pendleton Probe design using BaitFisher introns Nicrophorus vespilloides ref. genome transcriptomes single copy genes 1 2 3 WorkGlow – Target Capture Transcriptome assembly IdenBficaon of single copy & lyse bind wash elute orthologous loci probes single copy genes Transcriptome alignment Reference genome comparison Probe design using BaitFisher introns DNA extracBon of museum specimens Target capture & sequencing ReconstrucBon of phylogeny exBnct extant species species Morphology • finish matrix & score • idenBfy & include newly collected • Meet Dr Paweł Jałoszyński exBnct extant species species Scydmaeninae Morphology Target Capture • finish matrix & score • assemble transcriptomes • idenBfy & include newly collected • find orthologous genes across • Meet Dr Paweł Jałoszyński exBnct extant insects using annotated species species genomes • design & order probes • lab: DNA extracBons, target capture, sequencing Scydmaeninae Morphology Target Capture • finish matrix & score • assemble transcriptomes • idenBfy & include newly collected • find orthologous genes across • Meet Dr Paweł Jałoszyński exBnct extant insects using annotated species species genomes • design & order probes • lab: DNA extracBons, target capture, sequencing Scydmaeninae Finalize taxon sampling Morphology Target Capture • finish matrix & score • assemble transcriptomes • idenBfy & include newly collected • find orthologous genes across • Meet Dr Paweł Jałoszyński exBnct extant insects using annotated species species genomes • design & order probes • lab: DNA extracBons, target capture, sequencing Scydmaeninae Finalize taxon sampling PERL Introductory Course DidacBcs Course Responsible Conduct of Research Target Capture Course Side Project: Amber Fossils Baltic Amber Fossils 55 Mya at the beginning of the Eocene… • describe • draw & photograph • idenfy Dagmara Żyła Baltic Amber Fossils 1349-3 1349-3 1 cm Magnifcation 8x 1349-3 1349-3 1 cm Magnifcation 8x 1 cm 1 cm Magnifcation 5.6 x Magnifcation 5.6 x Dagmara Żyła Phylogenomics Bioinformacs Broad Morphology Range of skills Large Network Communicaon Skills Publicaons Presentaons Teaching Experience Phylogenomics Bioinformacs Broad Morphology Range of skills Positive Career Impact Large Network Communicaon Skills Publicaons Presentaons Teaching Experience This project has received funding from the European Union’s Horizon 2020 research and innovaon programme under the Marie Sklodowska-Curie grant agreement No 642241 What is the oldest known fossil? • Oldest really known fossils from Middle • Oldest known fossils from Late Triassic: Jurassic: 228-235 Ma (Chatzimanolis et al. 2012) 175-165 Ma (Cai, Huang, Thayer & Newton, 2012) Juroglypholoma anquum Leehermania prorova Staphylinid or Hydroscaphid Nicrophorus vespilloides Reference Genome & Transcriptome (Cunningham et al. 2015) Micropeplinae Empelinae Glypholomanae Microsilphinae Omaliinae Australophrum cribriceps Proteininae Silphotelus sp. Neophoninae Dasycerinae Protopselaphinae Pselaphinae Rybaxis longicornis Aleocharinae Aleochara curtula Transcriptomes Trichophyinae Habrocerinae Tachyporinae Sepedophilus testaceus Phoeocharinae Olisthaerinae Olisthaerus substriatus Scaphidiinae Scaphidium quadrimaculatum; Brachynopus scutellaris ApateBcinae PiesBnae Osoriinae Oxytelinae Trigonurinae Oxyporinae Megalopsidiinae Solieriinae Steninae EuaestheBnae Euaesthetus ruficapillus Scydmaeninae Euconnus hir7collis Leptotyphlinae Pseudopsinae Paederinae Oedichirus sp.; Paederus cruen7collis; Paederus Fuscipes Staphylininae Quedius diemenensis Ocypus brunnipes .
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