ena-STUDY-UNIVERSITY OF BASEL-20-07-2018-09:12:23:120-555
A phylogenomic study of the family Daphniidae
In the post-genomic era, much of the phylogenetic analyses still relies mainly on mitochondrial DNA or in combination with few nuclear genes. Although this approach often allows the construction of well-supported trees, it has the limitation that mtDNA describes the history of a single locus and that nuclear phylogenies based on a few loci may be biased, leading to inaccurate tree topologies and biased estimations of species divergence time. We performed a phylogenomic analysis of the family Daphniidae (Crustacea: Branchiopoda: Anomopoda), which includes some of the most frequently studied aquatic model organisms, Daphnia magna and D. pulex, yet whose phylogenetic relationships have been assessed mainly with few mtDNA genes. Using high-throughput sequencing we were able to assemble 38 whole mitochondrial genomes and draft nuclear genomes of 18 species, including at least one species for each known genus of the family Daphniidae. We present phylogenies based on 636 nuclear single-copy genes shared among all sampled taxa and based on whole mtDNA genomes. We obtained highly supported phylogenies, with some discrepancies between nuclear and mtDNA based trees for deeper nodes. We identified a new candidate sister lineage of Daphnia magna. Time-calibrated genomic trees using both fossil records and substitution rates resulted in very different estimates of branching event times when mtDNA is used. By providing multi-locus, fossil-calibrated trees of the Daphniidae, our study contributes to an improved phylogenetic framework for ecological and evolutionary studies using water fleas as a model system.
In the post-genomic era, much of the phylogenetic analyses still relies mainly on mitochondrial DNA or in combination with few nuclear genes. Although this approach often allows the construction of well-supported trees, it has the limitation that mtDNA describes the history of a single locus and that nuclear phylogenies based on a few loci may be biased, leading to inaccurate tree topologies and biased estimations of species divergence time. We performed a phylogenomic analysis of the family Daphniidae (Crustacea: Branchiopoda: Anomopoda), which includes some of the most frequently studied aquatic model organisms, Daphnia magna and D. pulex, yet whose phylogenetic relationships have been assessed mainly with few mtDNA genes. Using high-throughput sequencing we were able to assemble 38 whole mitochondrial genomes and draft nuclear genomes of 18 species, including at least one species for each known genus of the family Daphniidae. We present phylogenies based on 636 nuclear single-copy genes shared among all sampled taxa and based on whole mtDNA genomes. We obtained highly supported phylogenies, with some discrepancies between nuclear and mtDNA based trees for deeper nodes. We identified a new candidate sister lineage of Daphnia magna. Time-calibrated genomic trees using both fossil records and substitution rates resulted in very different estimates of branching event times when mtDNA is used. By providing multi-locus, fossil-calibrated trees of the Daphniidae, our study contributes to an improved phylogenetic framework for ecological and evolutionary studies using water fleas as a model system.