scholarly journals The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

2008 ◽  
Vol 363 (1496) ◽  
pp. 1435-1443 ◽  
Author(s):  
Kevin J Peterson ◽  
James A Cotton ◽  
James G Gehling ◽  
Davide Pisani
Keyword(s):  
Molecular Clock ◽  
Cambrian Explosion ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Historical Records ◽  
Calibration Point ◽  
Geological Time ◽  
Fossil Records

Unravelling the timing of the metazoan radiation is crucial for elucidating the macroevolutionary processes associated with the Cambrian explosion. Because estimates of metazoan divergence times derived from molecular clocks range from quite shallow (Ediacaran) to very deep (Mesoproterozoic), it has been difficult to ascertain whether there is concordance or quite dramatic discordance between the genetic and geological fossil records. Here, we show using a range of molecular clock methods that the major pulse of metazoan divergence times was during the Ediacaran, which is consistent with a synoptic reading of the Ediacaran macrobiota. These estimates are robust to changes in priors, and are returned with or without the inclusion of a palaeontologically derived maximal calibration point. Therefore, the two historical records of life both suggest that although the cradle of Metazoa lies in the Cryogenian, and despite the explosion of ecology that occurs in the Cambrian, it is the emergence of bilaterian taxa in the Ediacaran that sets the tempo and mode of macroevolution for the remainder of geological time.

scholarly journals Molecular clocks and the early evolution of metazoan nervous systems

2015 ◽  
Vol 370 (1684) ◽  
pp. 20150046 ◽  
Author(s):  
Gregory A. Wray
Keyword(s):  
Sensory Processing ◽  
Fossil Record ◽  
Sequence Data ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Sense Organs ◽  
Animal Evolution ◽  
Nervous Systems ◽  
Nervous System Evolution ◽  
Fossil Records

The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation.

scholarly journals Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation

2020 ◽  
Vol 12 (7) ◽  
pp. 1087-1098
Author(s):  
Alan J S Beavan ◽  
Philip C J Donoghue ◽  
Mark A Beaumont ◽  
Davide Pisani
Keyword(s):  
Molecular Clock ◽  
A Priori ◽  
Divergence Time ◽  
Time Estimation ◽  
Branch Length ◽  
Divergence Times ◽  
A Posteriori ◽  
Geological Time ◽  
Divergence Time Estimation ◽  
Relative Divergence

Abstract Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori appear to be less reliable than a priori calibrated, timescales.

scholarly journals Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Alejandra Serna-Sánchez ◽  
Oscar A. Pérez-Escobar ◽  
Diego Bogarín ◽  
María Fernanda Torres-Jimenez ◽  
Astrid Catalina Alvarez-Yela ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Phylogenetic Placement ◽  
Plastid Genomes ◽  
Phylogenetic Reconstructions ◽  
A Genome ◽  
Tree Models ◽  
Phylogenomic Analyses ◽  
First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

Central and Peripheral Clock Control of Circadian Feeding Rhythms

2021 ◽  
pp. 074873042110458
Author(s):  
Carson V. Fulgham ◽  
Austin P. Dreyer ◽  
Anita Nasseri ◽  
Asia N. Miller ◽  
Jacob Love ◽  
...  
Keyword(s):  
Locomotor Activity ◽  
Circadian Clock ◽  
Feeding Behavior ◽  
Molecular Clock ◽  
Fat Body ◽  
Molecular Clocks ◽  
Central Brain ◽  
Feeding Rhythms ◽  
Free Running ◽  
The Brain

Many behaviors exhibit ~24-h oscillations under control of an endogenous circadian timing system that tracks time of day via a molecular circadian clock. In the fruit fly, Drosophila melanogaster, most circadian research has focused on the generation of locomotor activity rhythms, but a fundamental question is how the circadian clock orchestrates multiple distinct behavioral outputs. Here, we have investigated the cells and circuits mediating circadian control of feeding behavior. Using an array of genetic tools, we show that, as is the case for locomotor activity rhythms, the presence of feeding rhythms requires molecular clock function in the ventrolateral clock neurons of the central brain. We further demonstrate that the speed of molecular clock oscillations in these neurons dictates the free-running period length of feeding rhythms. In contrast to the effects observed with central clock cell manipulations, we show that genetic abrogation of the molecular clock in the fat body, a peripheral metabolic tissue, is without effect on feeding behavior. Interestingly, we find that molecular clocks in the brain and fat body of control flies gradually grow out of phase with one another under free-running conditions, likely due to a long endogenous period of the fat body clock. Under these conditions, the period of feeding rhythms tracks with molecular oscillations in central brain clock cells, consistent with a primary role of the brain clock in dictating the timing of feeding behavior. Finally, despite a lack of effect of fat body selective manipulations, we find that flies with simultaneous disruption of molecular clocks in multiple peripheral tissues (but with intact central clocks) exhibit decreased feeding rhythm strength and reduced overall food intake. We conclude that both central and peripheral clocks contribute to the regulation of feeding rhythms, with a particularly dominant, pacemaker role for specific populations of central brain clock cells.

Understanding Molecular Clocks and Time Trees

2021 ◽  
pp. 326-337
Author(s):  
Andrew V. Z. Brower ◽  
Randall T. Schuh
Keyword(s):  
Amino Acid ◽  
Molecular Clock ◽  
Significant Error ◽  
Evolutionary Tree ◽  
Molecular Clocks ◽  
Amino Acid Substitutions ◽  
Absolute Minimum ◽  
Short Time ◽  
Over Time ◽  
Age Estimates

This chapter examines molecular clocks and time trees. Although laden with numerous process assumptions that may or may not be true (or knowable), the idea is appealingly straightforward: if amino acid substitutions in proteins occurred at a relatively steady pace that were more or less constant both over time and along each of the branches of a diverging evolutionary tree, then the number of substitutions would be directly related to the time since the taxa in question diverged from one another. However, evidence does not support a universal molecular clock. Evidence might or might not support “local” clocklike evolution among closely related taxa over relatively short time spans. Although absolute minimum ages for clades may be inferred from fossils, from biogeographical patterns, or extrapolated from secondary calibrations, such age estimates are subject to potentially significant error due to vagaries of geological dating as well as ambiguities of fossil identity. The test of a time tree hypothesis is to discover new fossil evidence that corroborates or falsifies it.

scholarly journals Age and rate of diversification of the Hawaiian silversword alliance (Compositae)

1998 ◽  
Vol 95 (16) ◽  
pp. 9402-9406 ◽  
Author(s):  
Bruce G. Baldwin ◽  
Michael J. Sanderson
Keyword(s):  
Common Ancestor ◽  
Error Variance ◽  
Diversification Rate ◽  
Recent Common Ancestor ◽  
Divergence Times ◽  
Sequence Evolution ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
Fossil Records ◽  
Fossil Data

Comparisons between insular and continental radiations have been hindered by a lack of reliable estimates of absolute diversification rates in island lineages. We took advantage of rate-constant rDNA sequence evolution and an “external” calibration using paleoclimatic and fossil data to determine the maximum age and minimum diversification rate of the Hawaiian silversword alliance (Compositae), a textbook example of insular adaptive radiation in plants. Our maximum-age estimate of 5.2 ± 0.8 million years ago for the most recent common ancestor of the silversword alliance is much younger than ages calculated by other means for the Hawaiian drosophilids, lobelioids, and honeycreepers and falls approximately within the history of the modern high islands (≤5.1 ± 0.2 million years ago). By using a statistically efficient estimator that reduces error variance by incorporating clock-based estimates of divergence times, a minimum diversification rate for the silversword alliance was estimated to be 0.56 ± 0.17 species per million years. This exceeds average rates of more ancient continental radiations and is comparable to peak rates in taxa with sufficiently rich fossil records that changes in diversification rate can be reconstructed.

scholarly journals The last Patagonian cycad,Austrozamiastockeyigen. et sp. nov., early Eocene of Laguna del Hunco, Chubut, Argentina

Botany ◽  
2016 ◽  
Vol 94 (9) ◽  
pp. 817-829 ◽  
Author(s):  
Peter Wilf ◽  
Dennis Wm. Stevenson ◽  
N. Rubén Cúneo
Keyword(s):  
Molecular Clock ◽  
Climate Changes ◽  
Terminal Phase ◽  
South American ◽  
Early Eocene ◽  
The Novel ◽  
Current Range ◽  
Extinct Genus ◽  
Fossil Records

The cycads pose classic problems in evolutionary biogeography, owing to their far-flung extant distributions and the sparse fossil records of living genera. A noteworthy example is Tribe Encephalarteae of Family Zamiaceae, today consisting of Encephalartos (Africa) and the Australian genera Lepidozamia and Macrozamia. Numerous petrified trunks of Encephalarteae described from the Cretaceous of Patagonia, Antarctica, and India indicate far larger past distributions across Gondwana and subsequent extinctions. The only fossils close to the current range are Paleogene leaf fragments from Australia assigned to Lepidozamia and Macrozamia. Here, we report a large frond piece and several isolated leaflets of a compressed cycad, along with an associated spiny petiole, from the late-Gondwanan, 52.2 Ma Laguna del Hunco flora of Patagonia, Argentina. Austrozamia stockeyi gen. et sp. nov., has the novel combination of an Encephalartos-type leaf and Lepidozamia-type cuticle. The Australian Lepidozamia fossils, widely used for molecular clock calibrations, could also represent an extinct genus. Austrozamia stockeyi demonstrates survival of the Encephalarteae in Patagonia and presumably across Gondwana until its terminal phase, adding a striking new component to the growing list of South American plant extinctions associated with Antarctic separation and related climate changes.

XVI.—Quantitative Evolution. III. Dp-ages of Gramineæ

1938 ◽  
Vol 57 ◽  
pp. 221-227
Author(s):  
James Small
Keyword(s):  
Time Scale ◽  
Evolutionary History ◽  
Geological Time ◽  
Exponential Curve ◽  
The Family ◽  
History Of ◽  
Geological Origin ◽  
Fossil Records

Applying Udny Yule's formulæ (1924) to the Compositæ, Small (1937) found that the average ages in doubling periods (Dp-ages) of the tribes of Compositæ, when plotted against a time-scale, gave points on an exponential curve called the BAT curve. If this curve is characteristic of average families of Angiosperms it should be possible to place the Dp-ages of tribes within other families on this curve as plotted against geological time, and thus obtain an order of geological origin which is quite independent of actual fossil records and which can be checked against any facts known concerning the evolutionary history of the family.

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