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 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 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.

Community Replacement Pathways: What Do Fossil Sequences Reveal About Marine Ecosystem Transitions?

1990 ◽  
Vol 5 ◽  
pp. 262-272
Author(s):  
William Miller
Keyword(s):  
Fossil Record ◽  
Large Scale ◽  
Marine Ecosystem ◽  
Small Scale ◽  
Data Sets ◽  
Mass Extinctions ◽  
Ultimate Cause ◽  
Long Time ◽  
History Of ◽  
Time And Energy

Paleontologists have lavished much time and energy on description and explanation of large-scale patterns in the fossil record (e.g., mass extinctions, histories of monophyletic taxa, deployment of major biogeographic units), while paying comparatively little attention to biologic patterns preserved only in local stratigraphic sequences. Interpretation of the large-scale patterns will always be seen as the chief justification for the science of paleontology, but solving problems framed by long time spans and large areas is rife with tenuous inference and patterns are prone to varied interpretation by different investigators using virtually the same data sets (as in the controversy over ultimate cause of the terminal Cretaceous extinctions). In other words, the large-scale patterns in the history of life are the true philosophical property of paleontology, but there will always be serious problems in attempting to resolve processes that transpired over millions to hundreds-of-millions of years and encompassed vast areas of seafloor or landscape. By contrast, less spectacular and more commonplace changes in local habitats (often related to larger-scale events and cycles) and attendant biologic responses are closer to our direct experience of the living world and should be easier to interpret unequivocally. These small-scale responses are reflected in the fossil record at the scale of local outcrops.

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.

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 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.

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 Fossilized cell structures identify an ancient origin for the teleost whole-genome duplication

2021 ◽  
Vol 118 (30) ◽  
pp. e2101780118
Author(s):  
Donald Davesne ◽  
Matt Friedman ◽  
Armin D. Schmitt ◽  
Vincent Fernandez ◽  
Giorgio Carnevale ◽  
...  
Keyword(s):  
Genome Size ◽  
Whole Genome Duplication ◽  
Large Scale ◽  
Genome Duplication ◽  
Bone Cell ◽  
Whole Genome ◽  
Crown Group ◽  
Stem Group ◽  
Genome Size Evolution ◽  
Stem Lineage

Teleost fishes comprise one-half of all vertebrate species and possess a duplicated genome. This whole-genome duplication (WGD) occurred on the teleost stem lineage in an ancient common ancestor of all living teleosts and is hypothesized as a trigger of their exceptional evolutionary radiation. Genomic and phylogenetic data indicate that WGD occurred in the Mesozoic after the divergence of teleosts from their closest living relatives but before the origin of the extant teleost groups. However, these approaches cannot pinpoint WGD among the many extinct groups that populate this 50- to 100-million-y lineage, preventing tests of the evolutionary effects of WGD. We infer patterns of genome size evolution in fossil stem-group teleosts using high-resolution synchrotron X-ray tomography to measure the bone cell volumes, which correlate with genome size in living species. Our findings indicate that WGD occurred very early on the teleost stem lineage and that all extinct stem-group teleosts known so far possessed duplicated genomes. WGD therefore predates both the origin of proposed key innovations of the teleost skeleton and the onset of substantial morphological diversification in the clade. Moreover, the early occurrence of WGD allowed considerable time for postduplication reorganization prior to the origin of the teleost crown group. This suggests at most an indirect link between WGD and evolutionary success, with broad implications for the relationship between genomic architecture and large-scale evolutionary patterns in the vertebrate Tree of Life.

scholarly journals Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds

2013 ◽  
Vol 280 (1768) ◽  
pp. 20131780 ◽  
Author(s):  
Roger B. J. Benson ◽  
Jonah N. Choiniere
Keyword(s):  
Adaptive Radiation ◽  
Large Scale ◽  
Crown Group ◽  
Deep Time ◽  
Diversification Rates ◽  
Stem Group ◽  
Key Innovation ◽  
Bird Evolution ◽  
Two Phases ◽  
Fossil Data

Birds are the most diverse living tetrapod group and are a model of large-scale adaptive radiation. Neontological studies suggest a radiation within the avian crown group, long after the origin of flight. However, deep time patterns of bird evolution remain obscure because only limited fossil data have been considered. We analyse cladogenesis and limb evolution on the entire tree of Mesozoic theropods, documenting the dinosaur–bird transition and immediate origins of powered flight. Mesozoic birds inherited constraints on forelimb evolution from non-flying ancestors, and species diversification rates did not accelerate in the earliest flying taxa. However, Early Cretaceous short-tailed birds exhibit both phenotypic release of the hindlimb and increased diversification rates, unparalleled in magnitude at any other time in the first 155 Myr of theropod evolution. Thus, a Cretaceous adaptive radiation of stem-group birds was enabled by restructuring of the terrestrial locomotor module, which represents a key innovation. Our results suggest two phases of radiation in Avialae: with the Cretaceous diversification overwritten by extinctions of stem-group birds at the Cretaceous–Palaeogene boundary, and subsequent diversification of the crown group. Our findings illustrate the importance of fossil data for understanding the macroevolutionary processes generating modern biodiversity.

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