@article{morlon_reconciling_2011,
Author = {Morlon, Hélène and Parsons, Todd L. and Plotkin,
Joshua B.},
Title = {Reconciling molecular phylogenies with the fossil
record},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {108},
Number = {39},
Pages = {16327--16332},
abstract = {Historical patterns of species diversity inferred from
phylogenies typically contradict the direct evidence
found in the fossil record. According to the fossil
record, species frequently go extinct, and many clades
experience periods of dramatic diversity loss. However,
most analyses of molecular phylogenies fail to identify
any periods of declining diversity, and they typically
infer low levels of extinction. This striking
inconsistency between phylogenies and fossils limits
our understanding of macroevolution, and it undermines
our confidence in phylogenetic inference. Here, we show
that realistic extinction rates and diversity
trajectories can be inferred from molecular
phylogenies. To make this inference, we derive an
analytic expression for the likelihood of a phylogeny
that accommodates scenarios of declining diversity,
time-variable rates, and incomplete sampling; we show
that this likelihood expression reliably detects
periods of diversity loss using simulation. We then
study the cetaceans (whales, dolphins, and porpoises),
a group for which standard phylogenetic inferences are
strikingly inconsistent with fossil data. When the
cetacean phylogeny is considered as a whole, recently
radiating clades, such as the Balaneopteridae,
Delphinidae, Phocoenidae, and Ziphiidae, mask the
signal of extinctions. However, when isolating these
groups, we infer diversity dynamics that are consistent
with the fossil record. These results reconcile
molecular phylogenies with fossil data, and they
suggest that most extant cetaceans arose from four
recent radiations, with a few additional species
arising from clades that have been in decline over the
last {\textasciitilde}10 Myr.},
doi = {10.1073/pnas.1102543108},
issn = {1091-6490},
language = {eng},
month = sep,
pmcid = {PMC3182748},
pmid = {21930899},
year = 2011
}
Author = {Morlon, Hélène and Parsons, Todd L. and Plotkin,
Joshua B.},
Title = {Reconciling molecular phylogenies with the fossil
record},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {108},
Number = {39},
Pages = {16327--16332},
abstract = {Historical patterns of species diversity inferred from
phylogenies typically contradict the direct evidence
found in the fossil record. According to the fossil
record, species frequently go extinct, and many clades
experience periods of dramatic diversity loss. However,
most analyses of molecular phylogenies fail to identify
any periods of declining diversity, and they typically
infer low levels of extinction. This striking
inconsistency between phylogenies and fossils limits
our understanding of macroevolution, and it undermines
our confidence in phylogenetic inference. Here, we show
that realistic extinction rates and diversity
trajectories can be inferred from molecular
phylogenies. To make this inference, we derive an
analytic expression for the likelihood of a phylogeny
that accommodates scenarios of declining diversity,
time-variable rates, and incomplete sampling; we show
that this likelihood expression reliably detects
periods of diversity loss using simulation. We then
study the cetaceans (whales, dolphins, and porpoises),
a group for which standard phylogenetic inferences are
strikingly inconsistent with fossil data. When the
cetacean phylogeny is considered as a whole, recently
radiating clades, such as the Balaneopteridae,
Delphinidae, Phocoenidae, and Ziphiidae, mask the
signal of extinctions. However, when isolating these
groups, we infer diversity dynamics that are consistent
with the fossil record. These results reconcile
molecular phylogenies with fossil data, and they
suggest that most extant cetaceans arose from four
recent radiations, with a few additional species
arising from clades that have been in decline over the
last {\textasciitilde}10 Myr.},
doi = {10.1073/pnas.1102543108},
issn = {1091-6490},
language = {eng},
month = sep,
pmcid = {PMC3182748},
pmid = {21930899},
year = 2011
}