Comprehensive Phylogeny of Ray-Finned Fishes Based on Transcriptomic and Genomic

Comprehensive phylogeny of ray-finned fishes based on transcriptomic and genomic

Lily C. Hughes (et al.)

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

• ~34,000 species, half of vertebrate diversity

• Molecular data overturned many previously hypothesized groups

• Genome sequencing for fishes has lagged behind other vertebrates (but we’re catching up)

• Fish-T1K was launched to produce transcriptomes across a diversity of fishes

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. • Produced 131 transcriptomes, which could be combined with already published transcriptomes and genomes to produce a matrix of 303 species for bony fishes with genomic resources

• Data Filtering: which molecular markers should be used?

• Data Analysis: how should we analyze large datasets?

• Hypothesis Testing: can we interrogate our dataset with previously

• Single-copy in 8 ray-finned fish genomes • >60% sequence identity & >200 bp = 1731 loci • Searched against 295 other transcriptomes & genomes of fishes

Vertebrate Genome Duplication

Vertebrate Teleost Genome Genome Duplication Duplication

Teleost Genome Duplication

Latimeria chalumnae • Constrained teleost, euteleost, and ostariophysan monophyly in each Polypterus bichir gene tree Acipenser sinensis Acipenser sinensis • Removed 469 loci with signal of Teleostei VGD Latimeria chalumnae • Removed additional 147 with signal 2018 © IIAcipenser Joint Congress on Evolutionarysinensis Biology 2018. All rights reserved - Any reproduction even in part is prohibited.of TGD Lepisosteus osseus Atractosteus spatula • Final dataset contained 1105 loci Amia calva that passed filters Teleostei

• 555,288 base pairs/185,096 amino acids

• 303 species

66/72 orders represented

Taxa •

• Analyzed DNA, Protein matrices with ExaML, ExaBayes, Astral

Loci2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

• Bootstrap support is generally high, but we wanted to explore some contentious clades in the literature, that were also contentious in our dataset

Elopomorpha

Base of Teleostei Osteoglossomorpha

Clupeocephala

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Hypothesis Testing Gene Genealogy Clupeocephala Interrogation Osteoglossomorpha Elopomorpha 1105 Gene Trees Osteoglossomorpha

Elopomorpha

Clupeocephala

Osteoglossomorpha

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Hypothesis Which topology is a better fit for each gene?Testing (GGI) Constrain AU Test 1105 Gene Trees Gene Trees Ranking

Clupeocephala Osteoglossomorpha Elopomorpha

Elopomorpha Clupeocephala

2018Osteoglossomorpha © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

• Many loci defined based on a few genomes may have undetected paralogs

• Phylogeny based on 303 species and 1105 loci is largely congruent with previous molecular hypotheses

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. • Phylogenomic analysis can mask conflicts in underlying gene tree distributions, but hypothesis testing can uncover support for alternative hypotheses

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Acknowledgements • Yong Zhang • Donald J. Stewart • Keith Crandall • Jun Zhao • Zhixiang Yan • Vanessa Gonzalez • Jose V. Lopez • Shanshan Liu • Elizabeth Alter • Kirk Kilfoyle • Yamin Huo • Adam Wong • Brad Pusey • Jing Zhang • Reviewers • Stephen Beatty • Nanxi Liu • GO Lab: Milton Tan, Victoria Rodriguez, Rose • Peter Rask Møller • Yadira Ortiz-Ruiz 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Peterson, Matthew • Mads Reinholdt • Robert Kallal Kolmann • Luiz Rocha • Jesus Ballesteros