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 Piesnae Glypholomanae Osoriinae 1 Piesnae Empelinae Omaliinae Megalopsidiinae Omaliine Habrocerinae Microsilphinae Group Trigunoridae Proteininae Trichophyinae Micropeplinae • conﬂicng Phloeocharinae 1 Neophoninae Scaphidiinae Dasycerinae • parally unresolved Apatecinae 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 Apatecinae Pselaphinae Scaphidiinae Dasycerinae Piesnae Neophoninae Osoriinae Osoriinae 2 Oxytelinae Phloeocharinae 2 Oxyporinae Aleocharinae Staphylinine Megalopsidiinae Scydmaeninae Group Steninae Solierinae Euaesthenae Euaesthenae 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 Piesnae Glypholomanae Osoriinae 1 Piesnae Empelinae Omaliinae Megalopsidiinae Omaliine Habrocerinae Microsilphinae Group Trigunoridae Proteininae Trichophyinae Micropeplinae • conﬂicng Phloeocharinae 1 Neophoninae Scaphidiinae Dasycerinae • parally unresolved Apatecinae 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 Apatecinae Pselaphinae Scaphidiinae Dasycerinae Piesnae Neophoninae Osoriinae Osoriinae 2 Oxytelinae Phloeocharinae 2 Oxyporinae Aleocharinae Staphylinine Megalopsidiinae Scydmaeninae Group Steninae Solierinae Euaesthenae Euaesthenae Solieriinae Steninae Leptotyphlinae Oxyporinae Pseudopsinae Leptotyphlinae Staphylininae Tachyporinae 2 Thayer 2005 Paederinae Silphidae aer McKenna et al. 2014 Worklow – Target Capture

lyse bind wash elute Worklow – Target Capture Transcriptome assembly

single reads - exons lyse bind wash elute

transcriptome Worklow – Target Capture Transcriptome assembly

single reads - exons Idenﬁcaon of single copy & lyse bind wash elute orthologous loci

transcriptome

Pendleton

Nicrophorus vespilloides ref. genome

single copy genes Worklow – Target Capture Transcriptome assembly

single reads - exons Idenﬁcaon of single copy & lyse bind wash elute orthologous loci

Transcriptome alignment

transcriptome

Pendleton

Nicrophorus vespilloides ref. genome

transcriptomes single copy genes 1 2 3 Worklow – Target Capture Transcriptome assembly

single reads - exons Idenﬁcaon of single copy & lyse bind wash elute orthologous loci

Transcriptome alignment

transcriptome Reference genome comparison

Pendleton

introns Nicrophorus vespilloides ref. genome

transcriptomes single copy genes 1 2 3 Worklow – Target Capture Transcriptome assembly

Idenﬁcaon of single copy & lyse bind wash elute orthologous loci probes

single copy genes Transcriptome alignment

Reference genome comparison

Pendleton Probe design using BaitFisher

introns Nicrophorus vespilloides ref. genome

transcriptomes single copy genes 1 2 3 Worklow – Target Capture Transcriptome assembly

Idenﬁcaon of single copy & lyse bind wash elute orthologous loci probes

single copy genes Transcriptome alignment

Reference genome comparison

Probe design using BaitFisher

introns DNA extracon of museum specimens

Target capture & sequencing

Reconstrucon of phylogeny exnct extant species species Morphology • ﬁnish matrix & score • idenfy & include newly collected • Meet Dr Paweł Jałoszyński exnct extant species species

Scydmaeninae Morphology Target Capture • ﬁnish matrix & score • assemble transcriptomes • idenfy & include newly collected • ﬁnd orthologous genes across • Meet Dr Paweł Jałoszyński exnct extant insects using annotated

species species genomes

• design & order probes

• lab: DNA extracons, target

capture, sequencing Scydmaeninae Morphology Target Capture • ﬁnish matrix & score • assemble transcriptomes • idenfy & include newly collected • ﬁnd orthologous genes across • Meet Dr Paweł Jałoszyński exnct extant insects using annotated

species species genomes

• design & order probes

• lab: DNA extracons, target

capture, sequencing Scydmaeninae

Finalize taxon sampling Morphology Target Capture • ﬁnish matrix & score • assemble transcriptomes • idenfy & include newly collected • ﬁnd orthologous genes across • Meet Dr Paweł Jałoszyński exnct extant insects using annotated

species species genomes

• design & order probes

• lab: DNA extracons, target

capture, sequencing Scydmaeninae

Finalize taxon sampling PERL Introductory Course

Didaccs 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

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 under programme innovaon -Curie Sklodowska the Marie 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 Apatecinae Piesnae Osoriinae Oxytelinae Trigonurinae

Oxyporinae Megalopsidiinae Solieriinae Steninae Euaesthenae Euaesthetus ruﬁcapillus Scydmaeninae Euconnus hircollis Leptotyphlinae Pseudopsinae Paederinae Oedichirus sp.; Paederus cruencollis; Paederus fuscipes Staphylininae Quedius diemenensis Ocypus brunnipes