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.

scholarly journals Tectonic calibrations in molecular dating

2011 ◽  
Vol 57 (1) ◽  
pp. 116-124 ◽  
Author(s):  
Ullasa Kodandaramaiah
Keyword(s):  
Analytical Methods ◽  
Molecular Dating ◽  
Circular Reasoning ◽  
Geological Process ◽  
Major Drawback ◽  
Minimum Age ◽  
Geological Event ◽  
Almost All ◽  
Geological Constraints ◽  
Age Estimates

Abstract Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeography are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously believed that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicariance in several groups. Moreover, the possibility of speciation having occurred before the said geological event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations always result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided.

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.

Eocene lantern fruits from Gondwanan Patagonia and the early origins of Solanaceae

Science ◽  
2017 ◽  
Vol 355 (6320) ◽  
pp. 71-75 ◽  
Author(s):  
Peter Wilf ◽  
Mónica R. Carvalho ◽  
María A. Gandolfo ◽  
N. Rubén Cúneo
Keyword(s):  
South America ◽  
Fossil Record ◽  
New World ◽  
Early Eocene ◽  
Ancient History ◽  
Cultural Importance ◽  
Early Diversification ◽  
Molecular Divergence ◽  
Divergence Dates

The nightshade family Solanaceae holds exceptional economic and cultural importance. The early diversification of Solanaceae is thought to have occurred in South America during its separation from Gondwana, but the family’s sparse fossil record provides few insights. We report 52.2-million-year-old lantern fruits from terminal-Gondwanan Patagonia, featuring highly inflated, five-lobed calyces, as a newly identified species of the derived, diverse New World genus Physalis (e.g., groundcherries and tomatillos). The fossils are considerably older than corresponding molecular divergence dates and demonstrate an ancient history for the inflated calyx syndrome. The derived position of these early Eocene fossils shows that Solanaceae were well diversified long before final Gondwanan breakup.

scholarly journals Evolution of seahorses' upright posture was linked to Oligocene expansion of seagrass habitats

2009 ◽  
Vol 5 (4) ◽  
pp. 521-523 ◽  
Author(s):  
Peter R. Teske ◽  
Luciano B. Beheregaray
Keyword(s):  
Fossil Record ◽  
Sequence Data ◽  
Morphological Evolution ◽  
Molecular Techniques ◽  
Molecular Dating ◽  
Upright Posture ◽  
Tectonic Events ◽  
Extant Species ◽  
The Family ◽  
Transitional Forms

Seahorses (Syngnathidae: Hippocampus ) are iconic marine teleosts that are readily identifiable by their upright posture. The fossil record is inadequate to shed light on the evolution of this trait because it lacks transitional forms. There are, however, extant syngnathid species (the pygmy pipehorses) that look like horizontally swimming seahorses and that might represent a surviving evolutionary link between the benthic seahorses and other, free-swimming members of the family Syngnathidae. Using sequence data from five nuclear loci, we confirm the sister taxon relationship between seahorses and pygmy pipehorses. Molecular dating indicates that the two taxa diverged during the Late Oligocene. During this time, tectonic events in the Indo-West Pacific resulted in the formation of vast amounts of new shallow-water areas and associated expansion of seagrass habitats that would have favoured the seahorses’ upright posture by improving their camouflage while not affecting their manoeuvrability negatively. The molecular techniques employed here provide new insights into the evolution of a taxon whose fossil record is incomplete, but whose evolutionary history is so recent that the major stages of morphological evolution are still represented in extant species.

scholarly journals Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
James A. Schulte
Keyword(s):  
Divergence Time ◽  
Penalized Likelihood ◽  
Molecular Data ◽  
Molecular Dating ◽  
Taxon Sampling ◽  
South American ◽  
The South ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Age Estimates

Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.

scholarly journals Jurassic primates, immobile ducks and other oddities: a reply to Heads’ review of The Monkey’s Voyage

2016 ◽  
Vol 29 (6) ◽  
pp. 403 ◽  
Author(s):  
Alan de Queiroz
Keyword(s):  
Fossil Record ◽  
A Priori ◽  
Molecular Dating ◽  
Long Distance Dispersal ◽  
Central Pacific ◽  
Long Distance ◽  
Reasonable Explanation

In The Monkey’s Voyage, I focused on the issue of disjunct distributions, and, in particular, on the burgeoning support from molecular-dating studies for long-distance dispersal over vicariance as the most reasonable explanation for many (but by no means all) distributions broken up by oceans. Michael Heads’ assessment of the book is founded on his long-standing belief, following Croizat, that long-distance dispersal is an insignificant process and, therefore, that disjunctions are virtually always attributable to vicariance. In holding to these notions, Heads offered a series of unsound arguments. In particular, to preserve an ‘all-vicariance’ perspective, he presented a distorted view of the nature of long-distance dispersal, misrepresented current applications of fossil calibrations in molecular-dating studies, ignored methodological biases in such studies that often favour vicariance hypotheses, repeatedly invoked irrelevant geological reconstructions, and, most strikingly, showed a cavalier approach to evolutionary timelines by pushing the origins of many groups back to unreasonably ancient ages. The result was a succession of implausible histories for particular taxa and areas, including the notions that the Hawaiian biota is almost entirely derived from ancient (often Mesozoic) central Pacific metapopulations, that the disjunctions of extremely mobile organisms such as ducks rarely, if ever, result from long-distance dispersal, and that primates were widespread 120 million years before their first appearance in the fossil record. In contrast to Heads’ perspective, a central message of The Monkey’s Voyage is that explanations for disjunct distributions should be evaluated on the basis of diverse kinds of evidence, without strong a priori assumptions about the relative likelihoods of long-distance dispersal and vicariance.

scholarly journals Using more than the oldest fossils: Dating Osmundaceae by three Bayesian clock approaches

2014 ◽  
Author(s):  
Guido Grimm ◽  
Pashalia Kapli ◽  
Benjamin Bomfleur ◽  
Stephen McLoughlin ◽  
Susanne S Renner
Keyword(s):  
Dna Sequences ◽  
Fossil Record ◽  
Morphological Characters ◽  
Genetic Distances ◽  
Total Evidence ◽  
Extinction Rates ◽  
Sister Clade ◽  
Extant Species ◽  
Dating Methods ◽  
Divergence Dates

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved--"node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv--to infer divergence times in the Osmundaceae or royal ferns. Osmundaceae have 13 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ~17 genera and three extinct families. For ND, we used the five oldest fossils, while for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizome and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence dates were generally greater than ages inferred from ND dating; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We favour the FBD-derived ages because they best match the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Palaeozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, FBD yielded 0.0299 (0.0099--0.0549) and 0.0240 (0.0039--0.0495) for these rates, whereas neontological data yielded 0.0314 and 0.0339. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling, therefore these estimates should be treated with caution.

scholarly journals Cretophengodidae, a new Cretaceous beetle family, sheds light on the evolution of bioluminescence

2021 ◽  
Vol 288 (1943) ◽  
pp. 20202730
Author(s):  
Yan-Da Li ◽  
Robin Kundrata ◽  
Erik Tihelka ◽  
Zhenhua Liu ◽  
Diying Huang ◽  
...  
Keyword(s):  
Fossil Record ◽  
Historical Biogeography ◽  
Tree Of Life ◽  
Light Organ ◽  
Defensive Function ◽  
Stem Group

Bioluminescent beetles of the superfamily Elateroidea (fireflies, fire beetles, glow-worms) are the most speciose group of terrestrial light-producing animals. The evolution of bioluminescence in elateroids is associated with unusual morphological modifications, such as soft-bodiedness and neoteny, but the fragmentary nature of the fossil record discloses little about the origin of these adaptations. We report the discovery of a new bioluminescent elateroid beetle family from the mid-Cretaceous of northern Myanmar ( ca 99 Ma), Cretophengodidae fam. nov. Cretophengodes azari gen. et sp. nov. belongs to the bioluminescent lampyroid clade, and would appear to represent a transitional fossil linking the soft-bodied Phengodidae + Rhagophthalmidae clade and hard-bodied elateroids. The fossil male possesses a light organ on the abdomen which presumably served a defensive function, documenting a Cretaceous radiation of bioluminescent beetles coinciding with the diversification of major insectivore groups such as frogs and stem-group birds. The discovery adds a key branch to the elateroid tree of life and sheds light on the evolution of soft-bodiedness and the historical biogeography of elateroid beetles.

scholarly journals A Miocene pygmy right whale fossil from Australia

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5025 ◽  
Author(s):  
Felix G. Marx ◽  
Travis Park ◽  
Erich M.G. Fitzgerald ◽  
Alistair R. Evans
Keyword(s):  
Southern Hemisphere ◽  
Late Miocene ◽  
External Morphology ◽  
Baleen Whales ◽  
Right Whale ◽  
Right Whales ◽  
Molecular Divergence ◽  
Living Species ◽  
Divergence Estimates ◽  
Single Living

Neobalaenines are an enigmatic group of baleen whales represented today by a single living species: the pygmy right whale, Caperea marginata, found only in the Southern Hemisphere. Molecular divergence estimates date the origin of pygmy right whales to 22–26 Ma, yet so far there are only three confirmed fossil occurrences. Here, we describe an isolated periotic from the latest Miocene of Victoria (Australia). The new fossil shows all the hallmarks of Caperea, making it the second-oldest described neobalaenine, and the oldest record of the genus. Overall, the new specimen resembles C. marginata in its external morphology and details of the cochlea, but is more archaic in it having a hypertrophied suprameatal area and a greater number of cochlear turns. The presence of Caperea in Australian waters during the Late Miocene matches the distribution of the living species, and supports a southern origin for pygmy right whales.

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