A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae

Show simple item record

dc.contributor.author Cornetti, Luca
dc.contributor.author Fields, Peter D.
dc.contributor.author Van Damme, Kay
dc.contributor.author Ebert, Dieter
dc.date.accessioned 2020-05-23T22:22:47Z
dc.date.available 2021-12-18T03:45:17Z
dc.date.issued 2019-08
dc.identifier.citation Cornetti , L , Fields , P D , Van Damme , K & Ebert , D 2019 , ' A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae ' , Molecular Phylogenetics and Evolution , vol. 137 , pp. 250-262 . https://doi.org/10.1016/j.ympev.2019.05.018
dc.identifier.other PURE: 126103850
dc.identifier.other PURE UUID: a32f0276-da04-4e64-8a97-349fce682798
dc.identifier.other WOS: 000472499000021
dc.identifier.uri http://hdl.handle.net/10138/315200
dc.description.abstract In the post-genomic era, much of phylogenetic analyses still relies on mitochondrial DNA, either alone or in combination with few nuclear genes. Although this approach often makes it possible to construct well-supported trees, it is limited because mtDNA describes the history of a single locus, and nuclear phylogenies based on a few loci may be biased, leading to inaccurate tree topologies and biased estimations of species divergence time. In this study, we perform a phylogenomic analysis of the Daphniidae family (Crustacea: Branchiopoda: Anomopoda) including some of the most frequently studied model organisms (Daphnia magna and D. pulex) whose phylogenetic relationships have been based primarily on an assessment of a few mtDNA genes. Using high-throughput sequencing, we were able to assemble 38 whole mitochondrial genomes and draft nuclear genomes for 18 species, including at least one species for each known genus of the family Daphniidae. Here we present phylogenies based on 636 nuclear single-copy genes shared among all sampled taxa and based on whole mtDNA genomes. The phylogenies we obtained were highly supported and showed some discrepancies between nuclear and mtDNA based trees at deeper nodes. We also identified a new candidate sister lineage of Daphnia magna. Our time-calibrated genomic trees, which we constructed using both fossil records and substitution rates, yielded very different estimates of branching event times compared to those based on mtDNA. By providing multi-locus, fossil-calibrated trees of the Daphniidae, our study contributes to an improved phylogenetic framework for ecological and evolutionary studies that use water fleas as a model system. en
dc.format.extent 13
dc.language.iso eng
dc.relation.ispartof Molecular Phylogenetics and Evolution
dc.rights cc_by_nc_nd
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject Substitution rates
dc.subject Fossil records
dc.subject Tree discrepancy
dc.subject Gene tree vs species tree
dc.subject Daphnia magna
dc.subject Daphnia pulex
dc.subject AMINO-ACID
dc.subject GENUS DAPHNIA
dc.subject EVOLUTION
dc.subject SELECTION
dc.subject GENOME
dc.subject 1181 Ecology, evolutionary biology
dc.subject 1182 Biochemistry, cell and molecular biology
dc.title A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae en
dc.type Article
dc.contributor.organization Tvärminne Zoological Station
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.1016/j.ympev.2019.05.018
dc.relation.issn 1055-7903
dc.rights.accesslevel openAccess
dc.type.version acceptedVersion

Files in this item

Total number of downloads: Loading...

Files Size Format View
Cornetti_etal_2 ... RS_ACCEPTED_MANUSCRIPT.pdf 1.544Mb PDF View/Open

This item appears in the following Collection(s)

Show simple item record