Described eukaryotic species in published species-level phylogenies: placement by molecular data, dates and date uncertainty
- 1Universita dellaSvizzera italiana (USI)
Abstract
Comparative analyses take published species-level phylogenies as data. Their estimates depend on how many described species a tree holds, how many were placed by sequence data, and whether the tree is dated with an uncertainty that can be carried into the analysis. These properties are reported one tree at a time, not on a common basis across eukaryotes. I divided the 2,085,869 described eukaryotic species into 60 groups and took the largest published species-level tree found for each of the 24 groups that have one. Resolving tips to Catalogue of Life accepted names, I counted species at four nested levels: in the tree, placed with molecular data, in a tree dated in absolute time, and in a dated tree whose archive carries date uncertainty (a set of dated trees or node intervals). I then fitted a constant-rate birth-death model to the 7 dated trees that hold taxonomically placed tips, pruned to their sequenced tips, with the sampling fraction that matches the pruned tree and with the full tree's fraction. The trees include 19.0% of described eukaryotic species, place 7.5% with molecular data and 5.4% in a dated tree. Date uncertainty is available for 1.1%, 38% of them in the tree of Birds; posterior or bootstrap datings of sequence data cover 0.64%. A tree the search did not find can only add to the 19.2% of described species named in any tree found. Keeping the full tree's fraction after pruning lowers the estimated speciation rate in every group, and puts the estimate on the boundary of zero extinction in 100 of 100 squamate and 95 of 100 amphibian posterior trees. A likelihood-ratio test of the full tree's fraction is made only on the 3 binary summary trees whose node ages come from a dating analysis (Fish, Mammals and Sharks); it rejects on none of them. A per-group table gives the largest tree found, its sequenced tips, what its archive carries for date uncertainty and the sampling fractions that match the full and the pruned tree. The sources of all 7 trees with taxonomically placed tips also distribute a tree of their sequenced species, 4 of them dated.
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BibTeX
@misc{richter2026described,
title = {{Described eukaryotic species in published species-level phylogenies: placement by molecular data, dates and date uncertainty}},
author = {F. Richter},
howpublished = {bioRxiv},
year = {2026},
month = may,
doi = {10.64898/2026.05.31.729127},
url = {https://www.biorxiv.org/content/10.64898/2026.05.31.729127v6},
note = {CC BY},
}
RIS
TY - UNPB
TI - Described eukaryotic species in published species-level phylogenies: placement by molecular data, dates and date uncertainty
AU - F. Richter
PY - 2026
DA - 2026/05/31
PB - bioRxiv
DO - 10.64898/2026.05.31.729127
UR - https://www.biorxiv.org/content/10.64898/2026.05.31.729127v6
AB - Comparative analyses take published species-level phylogenies as data. Their estimates depend on how many described species a tree holds, how many were placed by sequence data, and whether the tree is dated with an uncertainty that can be carried into the analysis. These properties are reported one tree at a time, not on a common basis across eukaryotes. I divided the 2,085,869 described eukaryotic species into 60 groups and took the largest published species-level tree found for each of the 24 groups that have one. Resolving tips to Catalogue of Life accepted names, I counted species at four nested levels: in the tree, placed with molecular data, in a tree dated in absolute time, and in a dated tree whose archive carries date uncertainty (a set of dated trees or node intervals). I then fitted a constant-rate birth-death model to the 7 dated trees that hold taxonomically placed tips, pruned to their sequenced tips, with the sampling fraction that matches the pruned tree and with the full tree's fraction. The trees include 19.0% of described eukaryotic species, place 7.5% with molecular data and 5.4% in a dated tree. Date uncertainty is available for 1.1%, 38% of them in the tree of Birds; posterior or bootstrap datings of sequence data cover 0.64%. A tree the search did not find can only add to the 19.2% of described species named in any tree found. Keeping the full tree's fraction after pruning lowers the estimated speciation rate in every group, and puts the estimate on the boundary of zero extinction in 100 of 100 squamate and 95 of 100 amphibian posterior trees. A likelihood-ratio test of the full tree's fraction is made only on the 3 binary summary trees whose node ages come from a dating analysis (Fish, Mammals and Sharks); it rejects on none of them. A per-group table gives the largest tree found, its sequenced tips, what its archive carries for date uncertainty and the sampling fractions that match the full and the pruned tree. The sources of all 7 trees with taxonomically placed tips also distribute a tree of their sequenced species, 4 of them dated.
ER -