scholarly journals Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record

2018 ◽  
Vol 285 (1881) ◽  
pp. 20181071 ◽  
Author(s):  
Michael S. Y. Lee ◽  
Adam M. Yates
Keyword(s):  
Molecular Clock ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Fossil Record ◽  
Character Evolution ◽  
Bayesian Approaches ◽  
Phylogenetic Methods ◽  
Divergence Dates ◽  
Divergence Estimates ◽  
Perfect Storm

Simultaneously analysing morphological, molecular and stratigraphic data suggests a potential resolution to a major remaining inconsistency in crocodylian evolution. The ancient, long-snouted thoracosaurs have always been placed near the Indian gharial Gavialis , but their antiquity ( ca 72 Ma) is highly incongruous with genomic evidence for the young age of the Gavialis lineage ( ca 40 Ma). We reconcile this contradiction with an updated morphological dataset and novel analysis, and demonstrate that thoracosaurs are an ancient iteration of long-snouted stem crocodylians unrelated to modern gharials. The extensive similarities between thoracosaurs and Gavialis are shown to be an almost ‘perfect storm’ of homoplasy, combining convergent adaptions to fish-eating, as well resemblances between genuinely primitive traits (thoracosaurs) and atavisms ( Gavialis ). Phylogenetic methods that ignore stratigraphy (parsimony and undated Bayesian methods) are unable to tease apart these similarities and invariably unite thoracosaurs and Gavialis. However, tip-dated Bayesian approaches additionally consider the large temporal gap separating ancient (thoracosaurs) and modern ( Gavialis ) iterations of similar long-snouted crocodyliforms. These analyses robustly favour a phylogeny which places thoracosaurs basal to crocodylians, far removed from modern gharials, which accordingly are a very young radiation. This phylogenetic uncoupling of ancient and modern gharial-like crocs is more consistent with molecular clock divergence estimates, and also the bulk of the crocodylian fossil record (e.g. all unequivocal gharial fossils are very young). Provided that the priors and models attribute appropriate relative weights to the morphological and stratigraphic signals—an issue that requires investigation—tip-dating approaches are potentially better able to detect homoplasy and improve inferences about phylogenetic relationships, character evolution and divergence dates.

scholarly journals Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships

2015 ◽  
Vol 282 (1812) ◽  
pp. 20150943 ◽  
Author(s):  
Mana Dembo ◽  
Nicholas J. Matzke ◽  
Arne Ø. Mooers ◽  
Mark Collard
Keyword(s):  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Taxonomic Status ◽  
Single Species ◽  
Methodological Issues ◽  
Bayesian Approaches ◽  
Phylogenetic Methods ◽  
Fossil Hominin ◽  
Future Work ◽  
The Relationship

The phylogenetic relationships of several hominin species remain controversial. Two methodological issues contribute to the uncertainty—use of partial, inconsistent datasets and reliance on phylogenetic methods that are ill-suited to testing competing hypotheses. Here, we report a study designed to overcome these issues. We first compiled a supermatrix of craniodental characters for all widely accepted hominin species. We then took advantage of recently developed Bayesian methods for building trees of serially sampled tips to test among hypotheses that have been put forward in three of the most important current debates in hominin phylogenetics—the relationship between Australopithecus sediba and Homo , the taxonomic status of the Dmanisi hominins, and the place of the so-called hobbit fossils from Flores, Indonesia, in the hominin tree. Based on our results, several published hypotheses can be statistically rejected. For example, the data do not support the claim that Dmanisi hominins and all other early Homo specimens represent a single species, nor that the hobbit fossils are the remains of small-bodied modern humans, one of whom had Down syndrome. More broadly, our study provides a new baseline dataset for future work on hominin phylogeny and illustrates the promise of Bayesian approaches for understanding hominin phylogenetic relationships.

scholarly journals Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

2014 ◽  
Vol 281 (1788) ◽  
pp. 20140677 ◽  
Author(s):  
Daniel T. Ksepka ◽  
Jessica L. Ware ◽  
Kristin S. Lamm
Keyword(s):  
Analytical Methods ◽  
Fossil Record ◽  
Tree Of Life ◽  
Temporal Information ◽  
Molecular Dating ◽  
Critical Nodes ◽  
Molecular Divergence ◽  
Divergence Dates ◽  
Divergence Estimates ◽  
Age Estimates

Major disparities are recognized between molecular divergence dates and fossil ages for critical nodes in the Tree of Life, but broad patterns and underlying drivers remain elusive. We harvested 458 molecular age estimates for the stem and crown divergences of 67 avian clades to explore empirical patterns between these alternate sources of temporal information. These divergence estimates were, on average, over twice the age of the oldest fossil in these clades. Mitochondrial studies yielded older ages than nuclear studies for the vast majority of clades. Unexpectedly, disparity between molecular estimates and the fossil record was higher for divergences within major clades (crown divergences) than divergences between major clades (stem divergences). Comparisons of dates from studies classed by analytical methods revealed few significant differences. Because true divergence ages can never be known with certainty, our study does not answer the question of whether fossil gaps or molecular dating error account for a greater proportion of observed disparity. However, empirical patterns observed here suggest systemic overestimates for shallow nodes in existing molecular divergence dates for birds. We discuss underlying biases that may drive these patterns.

A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa

Paleobiology ◽  
1998 ◽  
Vol 24 (4) ◽  
pp. 430-449 ◽  
Author(s):  
Peter J. Wagner
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
Fossil Record ◽  
Maximum Likelihood Method ◽  
Character Evolution ◽  
Likelihood Method ◽  
Data Sets ◽  
Data Set ◽  
Parsimony Tree ◽  
Tree Length

Estimates of phylogenetic relationships among fossil taxa implicitly provide hypotheses about the quality of the fossil record. Phylogenetic inferences also provide hypotheses about character evolution. The likelihood of any hypothesis that makes predictions about two data sets is simply the likelihood of the hypothesis given the first data set times the likelihood of the same hypothesis given the second data set. In this case, data set 1 represents stratigraphy and data set 2 represents morphology. Statistical methods exist for determining the likelihood of hypothesized levels of sampling. The likelihood of a hypothesized amount of character change yielding a particular most-parsimonious solution (i.e, L[hypothesized length | parsimony length] can be evaluated with simulations. A reanalysis of hyaenid phylogeny based on published character and stratigraphic data is presented here, using the maximum likelihood method. Two trees are found, depending on assumptions about ambiguous species, which are 11 and 10 steps longer than the most parsimonious tree (61 or 60 vs. 50 steps). However, the trees invoke far less stratigraphic debt (9 or 12 units vs. 47 units as measured in Mammal Zones). An important feature of the results is that the most likely tree length given hyaenid character data is estimated to be 56 to 62 steps (depending on the model of character evolution) rather than 50 steps. The likelihood tree suggests stronger trends toward bone-crushing specializations than does the parsimony tree and further suggests that high levels of homoplasy caused parsimony to underestimate the true extent of those trends. Simulations based on the character data and fossil record of hyaenids suggest that the maximum likelihood method is better able to estimate correct trees than is parsimony and somewhat better able to do so than previously proposed phylogenetic methods incorporating stratigraphy.

scholarly journals Multiple morphological clocks and total-evidence tip-dating in mammals

2016 ◽  
Vol 12 (7) ◽  
pp. 20160033 ◽  
Author(s):  
Michael S. Y. Lee
Keyword(s):  
Molecular Clock ◽  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Morphological Integration ◽  
Total Evidence ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Divergence Dates ◽  
Correlated Characters

Morphological integration predicts that correlated characters will coevolve; thus, each distinct suite of correlated characters might be expected to evolve according to a separate clock or ‘pacemaker’. Characters in a large morphological dataset for mammals were found to be evolving according to seven separate clocks, each distinct from the molecular clock. Total-evidence tip-dating using these multiple clocks inflated divergence time estimates, but potentially improved topological inference. In particular, single-clock analyses placed several meridiungulates and condylarths in a heterodox position as stem placentals, but multi-clock analyses retrieved a more plausible and orthodox position within crown placentals. Several shortcomings (including uneven character sampling) currently impact upon the accuracy of total-evidence dating, but this study suggests that when sufficiently large and appropriately constructed phenotypic datasets become more commonplace, multi-clock approaches are feasible and can affect both divergence dates and phylogenetic relationships.

Resolved phylogenetic relationships in the Ocotea complex ( Supraocotea ) facilitate phylogenetic classification and studies of character evolution

2021 ◽  
Vol 108 (4) ◽  
pp. 664-679
Author(s):  
Juan C. Penagos Zuluaga ◽  
Henk Werff ◽  
Brian Park ◽  
Deren A. R. Eaton ◽  
Liza S. Comita ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Character Evolution ◽  
Phylogenetic Classification

The fossil record of Phasmida (Insecta: Neoptera)

2000 ◽  
Vol 31 (4) ◽  
pp. 473-480 ◽  
Author(s):  
Erich Tilgner
Keyword(s):  
Dominican Republic ◽  
Molecular Clock ◽  
Fossil Record ◽  
Sister Group ◽  
Baltic Amber ◽  
Molecular Clock Dating

AbstractA review of the Phasmida fossil record is provided. No fossils of Timema Scudder are known. Euphasmida fossils include: Agathemera reclusa Scudder, Electrobaculum gracilis Sharov, Eophasma oregonense Sellick, Eophasma minor Sellick, Eophasmina manchesteri Sellick, Pseudoperla gracilipes Pictet, Pseudoperla lineata Pictet and various unclassified species from Grube Messel, Baltic amber, and Dominican Republic amber. The oldest documented Euphasmida fossils are 44-49 million years old; molecular clock dating underestimates the origin of the sister group Timema by at least 24 million years.

CAN BAYESIAN METHODS MAKE DATA AND ANALYSES MORE RELEVANT TO DECISION MAKERS?

2001 ◽  
Vol 17 (1) ◽  
pp. 114-122 ◽  
Author(s):  
Steven H. Sheingold
Keyword(s):  
Decision Making ◽  
Bayesian Methods ◽  
Paradigm Shift ◽  
Relevant Information ◽  
Decision Makers ◽  
Evidence Based ◽  
Critical Importance ◽  
Bayesian Approaches ◽  
Bayesian Analyses ◽  
And Performance

Decision making in health care has become increasingly reliant on information technology, evidence-based processes, and performance measurement. It is therefore a time at which it is of critical importance to make data and analyses more relevant to decision makers. Those who support Bayesian approaches contend that their analyses provide more relevant information for decision making than do classical or “frequentist” methods, and that a paradigm shift to the former is long overdue. While formal Bayesian analyses may eventually play an important role in decision making, there are several obstacles to overcome if these methods are to gain acceptance in an environment dominated by frequentist approaches. Supporters of Bayesian statistics must find more accommodating approaches to making their case, especially in finding ways to make these methods more transparent and accessible. Moreover, they must better understand the decision-making environment they hope to influence. This paper discusses these issues and provides some suggestions for overcoming some of these barriers to greater acceptance.

Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach

2013 ◽  
Vol 100 (5) ◽  
pp. 916-929 ◽  
Author(s):  
D. E. Soltis ◽  
M. E. Mort ◽  
M. Latvis ◽  
E. V. Mavrodiev ◽  
B. C. O'Meara ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Character Evolution ◽  
Evolution Analysis
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