Diversification dynamics of cheilostome bryozoans based on a Bayesian analysis of the fossil record

Palaeontology ◽  
2022 ◽  
Author(s):  
Farideh Moharrek ◽  
Paul D. Taylor ◽  
Daniele Silvestro ◽  
Helen L. Jenkins ◽  
Dennis P. Gordon ◽  
...  
Keyword(s):  
Bayesian Analysis ◽  
Fossil Record ◽  
Cheilostome Bryozoans

Competitive displacement among post-Paleozoic cyclostome and cheilostome bryozoans

Paleobiology ◽  
2000 ◽  
Vol 26 (1) ◽  
pp. 7-18 ◽  
Author(s):  
J. John Sepkoski ◽  
Frank K. McKinney ◽  
Scott Lidgard
Keyword(s):  
Mass Extinction ◽  
Fossil Record ◽  
Logistic Model ◽  
Competitive Interactions ◽  
Competitive Displacement ◽  
Critical Factors ◽  
History Of ◽  
Fossil Data ◽  
Cheilostome Bryozoans ◽  
Low Rate

Encrusting bryozoans provide one of the few systems in the fossil record in which ecological competition can be observed directly at local scales. The macroevolutionary history of diversity of cyclostome and cheilostome bryozoans is consistent with a coupled-logistic model of clade displacement predicated on species within clades interacting competitively. The model matches observed diversity history if the model is perturbed by a mass extinction with a position and magnitude analogous to the Cretaceous / Tertiary boundary event. Although it is difficult to measure all parameters in the model from fossil data, critical factors are intrinsic rates of extinction, which can be measured. Cyclostomes maintained a rather low rate of extinction the model solutions predict that they would lose diversity only slowly as competitively superior species of cheilostomes diversified into their environment. Thus, the microecological record of preserved competitive interactions between cyclostome and cheilostome bryozoans and the macroevolutionary record of global diversity are consistent in regard to competition as a significant influence on diversity histories of post-Paleozoic bryozoans.

scholarly journals Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record

2015 ◽  
Vol 207 (2) ◽  
pp. 425-436 ◽  
Author(s):  
Daniele Silvestro ◽  
Borja Cascales‐Miñana ◽  
Christine D. Bacon ◽  
Alexandre Antonelli
Keyword(s):  
Bayesian Analysis ◽  
Fossil Record ◽  
Vascular Plants

scholarly journals The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates

2017 ◽  
Author(s):  
Joseph W. Brown ◽  
Stephen A. Smith
Keyword(s):  
Bayesian Analysis ◽  
Early Cretaceous ◽  
Fossil Record ◽  
Divergence Time ◽  
Time Estimation ◽  
Inference Problem ◽  
Divergence Time Estimation ◽  
Divergence Time Estimates ◽  
The Impact ◽  
Pseudo Data

AbstractDivergence time estimation — the calibration of a phylogeny to geological time — is an integral first step in modelling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more. While the incompleteness of the fossil record is a common concern, issues of data limitation and model inadequacy are viable (if underexplored) alternative explanations. In this vein, Beaulieu et al. (2015) convincingly demonstrated how methods of divergence time inference can be misled by both (i) extreme state-dependent molecular substitution rate heterogeneity and (ii) biased sampling of representative major lineages. These results demonstrate the impact of (potentially common) model violations. Here, we suggest another potential challenge: that the configuration of the statistical inference problem (i.e., the parameters, their relationships, and associated priors) alone may preclude the reconstruction of the paleontological timeframe for the crown age of angiosperms. We demonstrate, through sampling from the joint prior (formed by combining the tree (diversification) prior with the calibration densities specified for fossil-calibrated nodes) that with no data present at all, that, an Early Cretaceous crown angiosperms is rejected (i.e., has essentially zero probability). More worrisome, however, is that, for the 24 nodes calibrated by fossils, almost all have indistinguishable marginal prior and posterior age distributions when employing routine lognormal fossil calibration priors. These results indicate that there is inadequate information in the data to overrule the joint prior. Given that these calibrated nodes are strategically placed in disparate regions of the tree, they act to anchor the tree scaffold, and so the posterior inference for the tree as a whole is largely determined by the pseudo-data present in the (often arbitrary) calibration densities. We recommend, as for any Bayesian analysis, that marginal prior and posterior distributions be carefully compared to determine whether signal is coming from the data or prior belief, especially for parameters of direct interest. This recommendation is not novel. However, given how rarely such checks are carried out in evolutionary biology, it bears repeating. Our results demonstrate the fundamental importance of prior/posterior comparisons in any Bayesian analysis, and we hope that they further encourage both researchers and journals to consistently adopt, this crucial step as standard practice. Finally, we note that the results presented here do not refute the biological modelling concerns identified by Beaulieu et al. (2015). Both sets of issues remain apposite to the goals of accurate divergence time estimation, and only by considering them in tandem can we move forward more confidently. [marginal priors; information content; diptych; divergence time estimation; fossil record; BEAST; angiosperms.]

Darwin's two competing phylogenetic trees: marsupials as ancestors or sister taxa?

2012 ◽  
Vol 39 (2) ◽  
pp. 217-233 ◽  
Author(s):  
J. David Archibald
Keyword(s):  
Fossil Record ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Charles Darwin ◽  
The Other ◽  
Charles Lyell ◽  
Single Origin ◽  
Molecular Studies ◽  
Richard Owen ◽  
First Time

Studies of the origin and diversification of major groups of plants and animals are contentious topics in current evolutionary biology. This includes the study of the timing and relationships of the two major clades of extant mammals – marsupials and placentals. Molecular studies concerned with marsupial and placental origin and diversification can be at odds with the fossil record. Such studies are, however, not a recent phenomenon. Over 150 years ago Charles Darwin weighed two alternative views on the origin of marsupials and placentals. Less than a year after the publication of On the origin of species, Darwin outlined these in a letter to Charles Lyell dated 23 September 1860. The letter concluded with two competing phylogenetic diagrams. One showed marsupials as ancestral to both living marsupials and placentals, whereas the other showed a non-marsupial, non-placental as being ancestral to both living marsupials and placentals. These two diagrams are published here for the first time. These are the only such competing phylogenetic diagrams that Darwin is known to have produced. In addition to examining the question of mammalian origins in this letter and in other manuscript notes discussed here, Darwin confronted the broader issue as to whether major groups of animals had a single origin (monophyly) or were the result of “continuous creation” as advocated for some groups by Richard Owen. Charles Lyell had held similar views to those of Owen, but it is clear from correspondence with Darwin that he was beginning to accept the idea of monophyly of major groups.

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