4 research outputs found
Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families
The evolution of new gene families subsequent to gene duplication may be coupled to the fluctuation of population and environment variables. Based upon that, we presented a systematic analysis of the animal transmembrane gene duplication events on a macroevolutionary scale by integrating the palaeontology repository. The age of duplication events was calculated by maximum likelihood method, and the age distribution was estimated by density histogram and normal kernel density estimation. We showed that the density of the duplicates displays a positive correlation with the estimates of maximum number of cell types of common ancestors, and the oxidation events played a key role in the major transitions of this density trace. Next, we focused on the Phanerozoic phase, during which more macroevolution data are available. The pulse mass extinction timepoints coincide with the local peaks of the age distribution, suggesting that the transmembrane gene duplicates fixed frequently when the environment changed dramatically. Moreover, a 61-million-year cycle is the most possible cycle in this phase by spectral analysis, which is consistent with the cycles recently detected in biodiversity. Our data thus elucidate a strong coupling of duplication events and macroevolution; furthermore, our method also provides a new way to address these questions
Long-term cycles in the history of life: Periodic biodiversity in the Paleobiology Database
Time series analysis of fossil biodiversity of marine invertebrates in the
Paleobiology Database (PBDB) shows a significant periodicity at approximately
63 My, in agreement with previous analyses based on the Sepkoski database. I
discuss how this result did not appear in a previous analysis of the PBDB. The
existence of the 63 My periodicity, despite very different treatment of
systematic error in both PBDB and Sepkoski databases strongly argues for
consideration of its reality in the fossil record. Cross-spectral analysis of
the two datasets finds that a 62 My periodicity coincides in phase by 1.6 My,
equivalent to better than the errors in either measurement. Consequently, the
two data sets not only contain the same strong periodicity, but its peaks and
valleys closely correspond in time. Two other spectral peaks appear in the PBDB
analysis, but appear to be artifacts associated with detrending and with the
increased interval length. Sampling-standardization procedures implemented by
the PBDB collaboration suggest that the signal is not an artifact of sampling
bias. Further work should focus on finding the cause of the 62 My periodicity.Comment: Published in PLoS ONE. 5 pages, 3 figures. Version with live links,
discussion available at
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004044#to
Considering the Case for Biodiversity Cycles: Reexamining the Evidence for Periodicity in the Fossil Record
Medvedev and Melott (2007) have suggested that periodicity in fossil
biodiversity may be induced by cosmic rays which vary as the Solar System
oscillates normal to the galactic disk. We re-examine the evidence for a 62
million year (Myr) periodicity in biodiversity throughout the Phanerozoic
history of animal life reported by Rohde & Mueller (2005), as well as related
questions of periodicity in origination and extinction. We find that the signal
is robust against variations in methods of analysis, and is based on
fluctuations in the Paleozoic and a substantial part of the Mesozoic.
Examination of origination and extinction is somewhat ambiguous, with results
depending upon procedure. Origination and extinction intensity as defined by RM
may be affected by an artifact at 27 Myr in the duration of stratigraphic
intervals. Nevertheless, when a procedure free of this artifact is implemented,
the 27 Myr periodicity appears in origination, suggesting that the artifact may
ultimately be based on a signal in the data. A 62 Myr feature appears in
extinction, when this same procedure is used. We conclude that evidence for a
periodicity at 62 Myr is robust, and evidence for periodicity at approximately
27 Myr is also present, albeit more ambiguous.Comment: Minor modifications to reflect final published versio