What to do with a billion years of evolution

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Alfred Gilmore
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1 What to do with a billion years of evolution Melissa DeBiasse University of Florida Whitney Laboratory for Marine melissa.debiasse@gmail.com melissadebiasse.weebly.com

2 Acknowledgements University of Florida Ryan Lab PI: Joseph Ryan Alexandra Hernandez Jessica Whelpley DEEPC PI: Steven Haddock Monterey Bay Aquarium Research Institute Darren Schultz Jacob Winnikoff PI: Erik Thuesen The Evergreen State College Telissa Wilson Warren Francis University of Southern Denmark Funding NSF Dimensions of Biodiversity (154679, , )

3 Porifera nophora Ctenophora Placozoa Cnidaria Bilateria Ctenophora nophora Porifera Animals Placozoa Cnidaria Bilateria Choanoflagellata Philippe et al. 009 Pick et al. 010 Nosenko et al. 013 Pisani et al. 015 Dunn et al. 008 Ryan et al. 013, Hejnol et al. 009 Moroz et al. 014, Chang et al. 015 Whelan et al. 015, Torruella et al. 015 Simion et al. 017 Feuda et al. 017 Borowiec et al. 015, Whelan et al. 017, Arcila et al. 017 Shen et al. 017

4 hora hora Choanoflagellata Porifera Animals Placozoa Cnidaria Bilateria Who cares? Accurate species trees are important tools for understanding evolutionary history Evolution of neural cell types

5 hora Ctenophora hora Porifera Placozoa Cnidaria Cnidaria Bilateria Bilateria Porifera x Choanoflagellata Choanoflagellata Choanoflagellata x x Animals Placozoa Cnidaria Bilateria 1 origin, 1 loss 1 origin, losses Ctenophora Ctenophora Ctenophora Porifera Animals Animals Placozoa Cnidaria Cnidaria Bilateria Bilateria Porifera Choanoflagellata Animals Porifera Placozoa Cnidaria Bilateria Choanoflagellata Choanoflagellata Choanoflagellata Animals Placozoa Cnidaria Bilateria origins origins Evolution of neural cell types

6 Species trees estimated over different time scales species complex in cardinals 10 mya relationships among insects 500 mya shallow introgression rapid radiation RADseq/UCEs nucleotide alignments gene tree / species tree methods past origin of multicellularity >1 billion mya time present deep ancient splits saturation compositional heterogeneity methods???

7 ophora nophora nophora nophora Ctenophora Ctenophora Choanoflagellata Choanoflagellata Porifera Porifera Animals Placozoa Bilateria Animals Placozoa Cnidaria Cnidaria crown group mya

8 Dimensions of Biodiversity DEEPC: Diversity, Ecology, EcoPhysiology of Ctenophores low high low high low high low high

9 Dimensions of Biodiversity DEEPC: Diversity, Ecology, EcoPhysiology of Ctenophores Comprehensive ctenophore species phylogeny Reconstruct ancestral depths Identify evolutionary depth transitions Test loci for convergent evolution to depth Link genotype to phenotype

10 Promoting transparency and overcoming bias in phylogenetics OUTLINE DECISIONS BEFORE RUNNING ANALYSES TRANSPARENCY ACCOUNTABILITY reproducability collaboration education Melissa DeBiasse Joseph Ryan & Melissa DeBiasse Whitney Laboratory for Marine Bioscience - Ryan Lab #154597

11 Data processing & analysis pipeline RNA-Seq

12 Data processing & analysis pipeline RNA-Seq Assemble & translate transcriptome CCGGAACGAGCACAGCCA PGRAQP

13 Data processing & analysis pipeline RNA-Seq Assemble & translate transcriptome Filter non-target sequences >Trinity_134 PGRAQPPGRAQPPGRAQP PVRNQADCHAQIPGMAFTI PGRAQPPGRAQPPGRAQP PVRNQADCHAQIPGMAFTI BLAST database metazoa non-metazoa

14 Data processing & analysis pipeline RNA-Seq Assemble & translate transcriptome Filter non-target sequences Identify orthologous loci

15 Orthologs: evolved from a common ancestor by speciation red cteno 1 gold cteno 1 Orthologs blue cteno 1a blue cteno 1b

16 Orthologs: evolved from a common ancestor by speciation Paralogs: produced through a duplication event red cteno 1 gold cteno 1 blue cteno 1a blue cteno 1b Paralogs

17 Orthologs: evolved from a common ancestor by speciation Paralogs: produced through a duplication event Orthogroup: orthologs and paralogs from MRCA red cteno 1 gold cteno 1 blue cteno 1a blue cteno 1b Orthogroup

18 colors = species numbers = genes

19 X 3 X gene loss 1 3 colors = species numbers = genes

20 gene duplication 1 3 colors = species numbers = genes

21 what are the ideal orthogroups?

22 orthogroup 1

23 orthogroup

24 orthogroup 3

25 identifying orthology complicated by gene dup. & loss, rate variation, HGT, contamination, etc

26 Splitting colors = species numbers = genes

27 Lumping colors = species numbers = genes

28 no. of orthogroups OrthoFinder number of species in an orthogroup

29 no. of orthogroups Splitting + translation artifacts number of species in an orthogroup

30 no. of orthogroups Splitting + gene loss number of species in an orthogroup

31 no. of orthogroups Lumping + single-copy orthogroups number of species in an orthogroup

32 no. of orthogroups OrthoFinder groups w/ paralogs groups w/ no paralogs number of species in o.g.

33 Orthogroup filtering colors = species numbers = genes 3 3

34 Orthogroup filtering Minimum number of taxa (80%) colors = species numbers = genes 3 3

35 Orthogroup filtering Minimum number of taxa (80%) colors = species numbers = genes 3 3

36 Orthogroup filtering Minimum number of taxa (80%) Max n paralogs per species in an orthogroup () colors = species numbers = genes 3 3

37 Orthogroup filtering Minimum number of taxa (80%) Max n paralogs per species in an orthogroup () colors = species numbers = genes 3 3

38 Orthogroup filtering Minimum number of taxa (80%) Max n paralogs per species in an orthogroup () colors = species numbers = genes 3 3

39 Orthogroup filtering Minimum number of taxa (80%) Max n paralogs per species in an orthogroup () PhyloTreePruner colors = species numbers = genes 3 3

40 Orthogroup filtering Minimum number of taxa (80%) Max n paralogs per species in an orthogroup () PhyloTreePruner colors = species numbers = genes X X

41 Orthogroup filtering colors = species numbers = genes

42 Align & concatenate single-copy orthogroups colors = species numbers = genes

43 Use data matrix to infer species phylogeny multi-locus concatenated species tree

44 PIPELINE Illumina Trinity TransDecoder Alien Index Orthofinder PhyloTreePruner custom script RAxML/IQ-TREE/PB RNA-Seq Assemble Translate Filter Orthogroups Paralogs Concatenate Tree >Trinity_1357 CCGGAACGAGCACAGCCA >Trinity_1357_pep PGRAQPWLIAPQRAWGLQR BLAST database metazoa non-metazoa X

45 Thank you Questions? Mnemiopsis leidyi photo: Joseph Ryan

Phylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?

Phylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species