scholarly journals The dynamics of stem and crown groups

2019 ◽  
Author(s):  
Graham E. Budd ◽  
Richard P. Mann
Keyword(s):  
Molecular Clock ◽  
Fossil Record ◽  
Null Hypothesis ◽  
Mass Extinctions ◽  
Crown Group ◽  
Stem Group ◽  
Group Members ◽  
Evolutionary Explanations ◽  
Birth Death

ABSTRACTThe fossil record of the origins of major groups is of great interests to many biologists, especially when the fossil record apparently conflicts with timings based on molecular clock estimates. Here we model the diversity of “stem” (basal) and “crown” (modern) members of groups as seen in the fossil record, using a “birth-death model”. Under background conditions, the stem group members must diversify rapidly until the modern crown group emerges, at which point their diversity rapidly collapses, followed shortly by their extinction. Mass extinctions can disturb this pattern to create very diverse stem groups such as the dinosaurs and trilobites. Understanding these null-hypothesis patterns is essential for framing ecological and evolutionary explanations for how major groups originate and subsequently evolve.

scholarly journals The dynamics of stem and crown groups

2020 ◽  
Vol 6 (8) ◽  
pp. eaaz1626 ◽  
Author(s):  
Graham E. Budd ◽  
Richard P. Mann
Keyword(s):  
Molecular Clock ◽  
Fossil Record ◽  
Large Scale ◽  
Mass Extinctions ◽  
Crown Group ◽  
Stem Group ◽  
Considerable Controversy ◽  
Long Stem ◽  
Evolutionary Explanations ◽  
Birth Death

The fossil record of the origins of major groups such as animals and birds has generated considerable controversy, especially when it conflicts with timings based on molecular clock estimates. Here, we model the diversity of “stem” (basal) and “crown” (modern) members of groups using a “birth-death model,” the results of which qualitatively match many large-scale patterns seen in the fossil record. Typically, the stem group diversifies rapidly until the crown group emerges, at which point its diversity collapses, followed shortly by its extinction. Mass extinctions can disturb this pattern and create long stem groups such as the dinosaurs. Crown groups are unlikely to emerge either cryptically or just before mass extinctions, in contradiction to popular hypotheses such as the “phylogenetic fuse”. The patterns revealed provide an essential context for framing ecological and evolutionary explanations for how major groups originate, and strengthen our confidence in the reliability of the fossil record.

scholarly journals Diversification dynamics of total-, stem-, and crown-groups are compatible with molecular clock estimates of divergence times

2021 ◽  
Vol 7 (24) ◽  
pp. eabf2257
Author(s):  
Alan J. S. Beavan ◽  
Davide Pisani ◽  
Philip C. J. Donoghue
Keyword(s):  
Time Scales ◽  
Molecular Clock ◽  
Fossil Record ◽  
Divergence Times ◽  
Evolutionary Time ◽  
Crown Group ◽  
Total Group ◽  
Fossil Evidence ◽  
Evolutionary Radiations ◽  
Birth Death

Molecular evolutionary time scales are expected to predate the fossil evidence, but, particularly for major evolutionary radiations, they can imply extremely protracted stem lineages predating the origin of living clades, leading to claims of systematic overestimation of divergence times. We use macroevolutionary birth-death models to describe the range of total-group and crown-group ages expected under constant rates of speciation and extinction. We extend current predictions on origination times for crown- and total-groups, and extinction of stem-groups, demonstrating that there is broad variance in these predictions. Under constant rates of speciation and extinction, we show that the distribution of expected arthropod total-group ages is consistent with molecular clock estimates. The fossil record cannot be read literally, and our results preclude attempts to interpret the antiquity of clades based on the co-occurrence of stem- and crown-representatives.

scholarly journals The fossil record of early eukaryotic diversification

2004 ◽  
Vol 10 ◽  
pp. 35-50 ◽  
Author(s):  
Susannah M. Porter
Keyword(s):  
Fossil Record ◽  
Main Phase ◽  
Cambrian Explosion ◽  
Evolution Of Sex ◽  
Crown Group ◽  
Long Period ◽  
Stem Group ◽  
Group Evolution ◽  
Domains Of Life ◽  
Ecology And Environment

The Cambrian explosion can be thought of as the culmination of a diversification of eukaryotes that had begun several hundred million years before. Eukaryotes - one of the three domains of life — originated by late Archean time, and probably underwent a long period of stem group evolution during the Paleoproterozoic Era. A suite of taxonomically resolved body fossils and biomarkers, together with estimates of acritarch and compression fossil diversity, suggest that while divergences among major eukaryotic clades or 'super-groups' may have occurred as early as latest Paleoproterozoic through Mesoproterozoic time, the main phase of eukaryotic diversification took place several hundred million years later, during the middle Neoproterozoic Era. Hypotheses for Neoproterozoic diversification must therefore explain why eukaryotic diversification is delayed several hundred million years after the origin of the eukaryotic crown group, and why diversification appears to have occurred independently within several eukaryotic super-groups at the same time. Evolutionary explanations for eukaryotic diversification (the evolution of sex; the acquisition of plastids) fail to account for these patterns, but ecological explanations (the advent of microbial predators) and environmental explanations (changes in ocean chemistry) are both consistent with them. Both ecology and environment may have played a role in triggering or at least fueling Neoproterozoic eukaryotic diversification.

On the statistical detection of cycles in extinctions in the marine fossil record

Paleobiology ◽  
1987 ◽  
Vol 13 (4) ◽  
pp. 465-478 ◽  
Author(s):  
James F. Quinn
Keyword(s):  
Fossil Record ◽  
Null Hypothesis ◽  
Time Lags ◽  
Mass Extinctions ◽  
A Posteriori ◽  
Alternative Analysis ◽  
Extinction Rates ◽  
Statistical Detection ◽  
Definition Of ◽  
Parameter Estimation Techniques

Periodicity has recently been reported in the extinction rates of fossil marine families since the Permian. The analysis used appears particularly sensitive to parameter estimation techniques, particularly in the definition of mass extinctions. It also fails to incorporate autocorrelation in the fossil record into its null hypothesis and rests on an inappropriate a posteriori comparison to the null hypothesis. An alternative analysis, examining the time-lags between periods of high extinction rates, produces no evidence of a cycle.

scholarly journals New mid-Cretaceous cryptic slime mold beetles and the early evolution of Sphindidae (Coleoptera: Cucujoidea)

2021 ◽  
Vol 79 ◽  
pp. 587-597
Author(s):  
Yan-Da Li ◽  
Erik Tihelka ◽  
Zhen-Hua Liu ◽  
Di-Ying Huang ◽  
Chen‑Yang Cai
Keyword(s):  
Phylogenetic Analysis ◽  
Fossil Record ◽  
Slime Mold ◽  
Early Evolution ◽  
Calibration Point ◽  
Crown Group ◽  
Slime Molds ◽  
The Family ◽  
Group Members

Abstract The cryptic slime mold beetles, Sphindidae, are a moderately diverse cucujoid beetle family, whose members are obligately tied to slime molds throughout their life. The fossil record of sphindid beetles is sparse; stem-sphindids and crown-group members of uncertain systematic placement have been reported from Cretaceous ambers. Here we review the Mesozoic fossil record of Sphindidae and report a new sphindid genus and species, Trematosphindus newtonigen. et sp. nov., from Albian/Cenomanian amber from northern Myanmar (ca. 99 Ma). Trematosphindus is set apart from all other sphindids by the presence of distinct lateral cavities on the anterior pronotal angles. Our phylogenetic analysis identifies Trematosphindus as an early-diverging genus within Sphindidae, sister to the remainder of the family except Protosphindus, or Protosphindus and Odontosphindus. The new fossils provide evidence that basal crown slime mold beetles begun to diversify by the mid-Cretaceous, providing a valuable calibration point for understanding timescale of sphindid co-evolution with slime molds.

scholarly journals Horizontal Gene Transfer Constrains the Timing of Methanogen Evolution

2017 ◽  
Author(s):  
Joanna M. Wolfe ◽  
Gregory P. Fournier
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Clock ◽  
Methane Production ◽  
Fossil Record ◽  
Early Earth ◽  
Crown Group ◽  
Temporal Constraint ◽  
Lower Luminosity ◽  
Time Evaluation

ABSTRACTMicrobial methanogenesis may have been a major component of Earth’s carbon cycle during the Archaean Eon, generating a methane greenhouse that increased global temperatures enough for a liquid hydrosphere, despite the sun’s lower luminosity at the time. Evaluation of potential solutions to the “faint young sun” hypothesis by determining the age of microbial methanogenesis was limited by ambiguous geochemical evidence, and the absence of a diagnostic fossil record. To overcome these challenges, we utilize a temporal constraint: a horizontal gene transfer (HGT) event from within archaeal methanogens to the ancestor of Cyanobacteria, one of the few microbial clades with recognized crown group fossils. Results of molecular clock analyses calibrated by this HGT-propagated constraint show methanogens diverging within Euryarchaeota no later than 3.51 Ga, with methanogenesis itself likely evolving earlier. This timing provides independent support for scenarios wherein microbial methane production was important in maintaining temperatures on the early Earth.

scholarly journals Aquatic stem group myriapods close a gap between molecular divergence dates and the terrestrial fossil record

2020 ◽  
Vol 117 (16) ◽  
pp. 8966-8972 ◽  
Author(s):  
Gregory D. Edgecombe ◽  
Christine Strullu-Derrien ◽  
Tomasz Góral ◽  
Alexander J. Hetherington ◽  
Christine Thompson ◽  
...  
Keyword(s):  
Fossil Record ◽  
Hot Spring ◽  
Sister Group ◽  
Head Capsule ◽  
The Body ◽  
Molecular Dating ◽  
Crown Group ◽  
Stem Group ◽  
Small Set ◽  
Body Fossil

Identifying marine or freshwater fossils that belong to the stem groups of the major terrestrial arthropod radiations is a longstanding challenge. Molecular dating and fossils of their pancrustacean sister group predict that myriapods originated in the Cambrian, much earlier than their oldest known fossils, but uncertainty about stem group Myriapoda confounds efforts to resolve the timing of the group’s terrestrialization. Among a small set of candidates for membership in the stem group of Myriapoda, the Cambrian to Triassic euthycarcinoids have repeatedly been singled out. The only known Devonian euthycarcinoid, Heterocrania rhyniensis from the Rhynie and Windyfield cherts hot spring complex in Scotland, reveals details of head structures that constrain the evolutionary position of euthycarcinoids. The head capsule houses an anterior cuticular tentorium, a feature uniquely shared by myriapods and hexapods. Confocal microscopy recovers myriapod-like characters of the preoral chamber, such as a prominent hypopharynx supported by tentorial bars and superlinguae between the mandibles and hypopharynx, reinforcing an alliance between euthycarcinoids and myriapods recovered in recent phylogenetic analysis. The Cambrian occurrence of the earliest euthycarcinoids supplies the oldest compelling evidence for an aquatic stem group for either Myriapoda or Hexapoda, previously a lacuna in the body fossil record of these otherwise terrestrial lineages until the Silurian and Devonian, respectively. The trace fossil record of euthycarcinoids in the Cambrian and Ordovician reveals amphibious locomotion in tidal environments and fills a gap between molecular estimates for myriapod origins in the Cambrian and a post-Ordovician crown group fossil record.

scholarly journals History is written by the victors: the effect of the push of the past on the fossil record

2017 ◽  
Author(s):  
Graham E. Budd ◽  
Richard P. Mann
Keyword(s):  
Fossil Record ◽  
Molecular Clocks ◽  
Phenotypic Evolution ◽  
Mass Extinctions ◽  
The Past ◽  
Extinction Rates ◽  
The Mean ◽  
Birth Death

AbstractPhylogenies may be modelled using “birth-death” models for speciation and extinction, but even when a homogeneous rate of diversification is used, survivorship biases can generate remarkable rate heterogeneities through time. One such bias has been termed the “push of the past”, by which the length of time a clade has survived is conditioned on the rate of diversification that happened to pertain at its origin. This creates the illusion of a secular rate slow-down through time that is, rather, a reversion to the mean. Here we model the controls on the push of the past, and the effect it has on clade origination times, and show that it largely depends on underlying extinction rates. An extra effect increasing early rates of lineage generation is also seen in large clades. These biases are important but relatively neglected influences on many aspects of diversification patterns, such as diversification spikes after mass extinctions and at the origins of clades; they also influence rates of fossilisation, changes in rates of phenotypic evolution and even molecular clocks. These inevitable features of surviving and/or large clades should thus not be generalised to the diversification process as a whole without additional study of small and extinct clades.

scholarly journals Fossil evidence unveils an early Cambrian origin for Bryozoa

Nature ◽  
2021 ◽  
Author(s):  
Zhiliang Zhang ◽  
Zhifei Zhang ◽  
Junye Ma ◽  
Paul D. Taylor ◽  
Luke C. Strotz ◽  
...  
Keyword(s):  
South China ◽  
Molecular Clock ◽  
Fossil Record ◽  
Phylogenetic Analyses ◽  
Early Cambrian ◽  
Modular Construction ◽  
Organic Composition ◽  
Stem Group ◽  
Lower Ordovician ◽  
First Occurrence

AbstractBryozoans (also known as ectoprocts or moss animals) are aquatic, dominantly sessile, filter-feeding lophophorates that construct an organic or calcareous modular colonial (clonal) exoskeleton1–3. The presence of six major orders of bryozoans with advanced polymorphisms in lower Ordovician rocks strongly suggests a Cambrian origin for the largest and most diverse lophophorate phylum2,4–8. However, a lack of convincing bryozoan fossils from the Cambrian period has hampered resolution of the true origins and character assembly of the earliest members of the group. Here we interpret the millimetric, erect, bilaminate, secondarily phosphatized fossil Protomelission gatehousei9 from the early Cambrian of Australia and South China as a potential stem-group bryozoan. The monomorphic zooid capsules, modular construction, organic composition and simple linear budding growth geometry represent a mixture of organic Gymnolaemata and biomineralized Stenolaemata character traits, with phylogenetic analyses identifying P. gatehousei as a stem-group bryozoan. This aligns the origin of phylum Bryozoa with all other skeletonized phyla in Cambrian Age 3, pushing back its first occurrence by approximately 35 million years. It also reconciles the fossil record with molecular clock estimations of an early Cambrian origination and subsequent Ordovician radiation of Bryozoa following the acquisition of a carbonate skeleton10–13.

A partial lower jaw of a tetrapod from “Romer's Gap”

2017 ◽  
Vol 108 (1) ◽  
pp. 55-65 ◽  
Author(s):  
Donglei Chen ◽  
Yasaman Alavi ◽  
Martin D. Brazeau ◽  
Henning Blom ◽  
David Millward ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Lateral Line ◽  
Early Carboniferous ◽  
Crown Group ◽  
Distinctive Character ◽  
Lower Jaw ◽  
Stem Group ◽  
Significant Step ◽  
Group Members

ABSTRACTThe first half of the Mississippian or Early Carboniferous (Tournaisian to mid- Viséan), an interval of about 20 million years, has become known as “Romer's Gap” because of its poor tetrapod record. Recent discoveries emphasise the differences between pre-“Gap” Devonian tetrapods, unambiguous stem-group members retaining numerous “fish” characters indicative of an at least partially aquatic lifestyle, and post-“Gap” Carboniferous tetrapods, which are far more diverse and include fully terrestrial representatives of the main crown-group lineages. It seems that “Romer's Gap” coincided with the cladogenetic events leading to the origin of the tetrapod crown group. Here, we describe a partial right lower jaw ramus of a tetrapod from the late Tournaisian or early Viséan of Scotland. The large and robust jaw displays a distinctive character combination, including a significant mesial lamina of the strongly sculptured angular, an open sulcus for the mandibular lateral line, a non-ossified narrow Meckelian exposure, a well-defined dorsal longitudinal denticle ridge on the prearticular, and a mesially open adductor fossa. A phylogenetic analysis places this specimen in a trichotomy withCrassigyrinusand baphetids + higher tetrapods in the upper part of the tetrapod stem group, aboveWhatcheeria, Pederpes,Ossinodus,SigourneaandGreererpeton. It represents a small but significant step in the gradual closure of “Romer's Gap”.

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