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 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 Early fossil record of Euarthropoda and the Cambrian Explosion

2018 ◽  
Vol 115 (21) ◽  
pp. 5323-5331 ◽  
Author(s):  
Allison C. Daley ◽  
Jonathan B. Antcliffe ◽  
Harriet B. Drage ◽  
Stephen Pates
Keyword(s):  
Fossil Record ◽  
Trace Fossils ◽  
Cambrian Explosion ◽  
Burgess Shale ◽  
Crown Group ◽  
Total Group ◽  
Stem Lineage ◽  
Coherent Picture ◽  
Insight Into ◽  
Phosphate Deposits

Euarthropoda is one of the best-preserved fossil animal groups and has been the most diverse animal phylum for over 500 million years. Fossil Konservat-Lagerstätten, such as Burgess Shale-type deposits (BSTs), show the evolution of the euarthropod stem lineage during the Cambrian from 518 million years ago (Ma). The stem lineage includes nonbiomineralized groups, such as Radiodonta (e.g., Anomalocaris) that provide insight into the step-by-step construction of euarthropod morphology, including the exoskeleton, biramous limbs, segmentation, and cephalic structures. Trilobites are crown group euarthropods that appear in the fossil record at 521 Ma, before the stem lineage fossils, implying a ghost lineage that needs to be constrained. These constraints come from the trace fossil record, which show the first evidence for total group Euarthropoda (e.g., Cruziana, Rusophycus) at around 537 Ma. A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma). This constrains the appearance of the euarthropod stem lineage to no older than 550 Ma. While each of the major types of fossil evidence (BSTs, trace fossils, and biomineralized preservation) have their limitations and are incomplete in different ways, when taken together they allow a coherent picture to emerge of the origin and subsequent radiation of total group Euarthropoda during the Cambrian.

scholarly journals The evolution of methods for establishing evolutionary timescales

2016 ◽  
Vol 371 (1699) ◽  
pp. 20160020 ◽  
Author(s):  
Philip C. J. Donoghue ◽  
Ziheng Yang
Keyword(s):  
Fossil Record ◽  
Environmental Influence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Fossil Species ◽  
Time Estimates ◽  
Fossil Evidence ◽  
Probability Densities ◽  
History Of ◽  
Lineage Divergence

The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

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.

It's a protist-eat-protist world: recalcitrance, predation, and evolution in the Tonian–Cryogenian ocean

2018 ◽  
Vol 2 (2) ◽  
pp. 173-180 ◽  
Author(s):  
Phoebe A. Cohen ◽  
Leigh Anne Riedman
Keyword(s):  
Molecular Clock ◽  
Fossil Record ◽  
Critical Role ◽  
Indirect Evidence ◽  
Tree Of Life ◽  
Current Understanding ◽  
Evolutionary Transitions ◽  
Ecological Interaction ◽  
Fossil Evidence ◽  
Multiple Metrics

Predation, and how organisms respond to it, is an important ecological interaction across the tree of life. Much of our understanding of predation focuses on modern metazoa. However, predation is equally important in single-celled eukaryotes (commonly referred to as protists). In the fossil record, we see evidence of protists preying on other protists beginning in the Tonian Period (1000–720 Ma). In addition, the first evidence of eukaryotic biomineralization and the appearance of multiple unmineralized but recalcitrant forms are also seen in the Tonian and Cryogenian (720–635 Ma), potentially indirect evidence of predation. This fossil evidence, coupled with molecular clock analyses, is coincident with multiple metrics that show an increase in the diversity of eukaryotic clades and fossil assemblages. Predation, thus, may have played a critical role in the diversification of eukaryotes and the evolution of protistan armor in the Neoproterozoic Era. Here, we review the current understanding of predation in the Tonian and Cryogenian oceans as viewed through the fossil record, and discuss how the rise of eukaryotic predation upon other eukaryotes (eukaryovory) may have played a role in major evolutionary transitions including the origins of biomineralization.

scholarly journals A molecular palaeobiological exploration of arthropod terrestrialization

2016 ◽  
Vol 371 (1699) ◽  
pp. 20150133 ◽  
Author(s):  
Jesus Lozano-Fernandez ◽  
Robert Carton ◽  
Alastair R. Tanner ◽  
Mark N. Puttick ◽  
Mark Blaxter ◽  
...  
Keyword(s):  
Divergence Times ◽  
Crown Group ◽  
Terrestrial Arthropods ◽  
Biological Adaptation ◽  
Fossil Evidence ◽  
History Of ◽  
Terrestrial Fungi ◽  
Terrestrial Biodiversity ◽  
Body Fossil ◽  
Colonization Of Land

Understanding animal terrestrialization, the process through which animals colonized the land, is crucial to clarify extant biodiversity and biological adaptation. Arthropoda (insects, spiders, centipedes and their allies) represent the largest majority of terrestrial biodiversity. Here we implemented a molecular palaeobiological approach, merging molecular and fossil evidence, to elucidate the deepest history of the terrestrial arthropods. We focused on the three independent, Palaeozoic arthropod terrestrialization events (those of Myriapoda, Hexapoda and Arachnida) and showed that a marine route to the colonization of land is the most likely scenario. Molecular clock analyses confirmed an origin for the three terrestrial lineages bracketed between the Cambrian and the Silurian. While molecular divergence times for Arachnida are consistent with the fossil record, Myriapoda are inferred to have colonized land earlier, substantially predating trace or body fossil evidence. An estimated origin of myriapods by the Early Cambrian precedes the appearance of embryophytes and perhaps even terrestrial fungi, raising the possibility that terrestrialization had independent origins in crown-group myriapod lineages, consistent with morphological arguments for convergence in tracheal systems. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

A Paleozoic stem hagfish Myxinikela siroka — revised anatomy and implications for evolution of the living jawless vertebrate lineages

2020 ◽  
Vol 98 (12) ◽  
pp. 850-865
Author(s):  
Tetsuto Miyashita
Keyword(s):  
Soft Tissue ◽  
Fossil Record ◽  
Estuarine System ◽  
Single Specimen ◽  
Calibration Point ◽  
Crown Group ◽  
Total Group ◽  
Posterior Displacement ◽  
Well Differentiated ◽  
Branchial Region

Hagfishes and lampreys comprise cyclostomes, the earliest branching and sole surviving clade of the once diverse assemblage of jawless crown-group vertebrates. Lacking mineralized skeletons, both of the crown cyclostome lineages have notoriously poor fossil record. Particularly in the hagfish total group, †Myxinikela siroka Bardack, 1991 from the Late Carboniferous estuarine system of Illinois (USA) represents the only definitive stem taxon. Previously known from a single specimen, Myxinikela has been reconstructed as a short-bodied form with pigmented eyes but otherwise difficult to distinguish from the living counterpart. With a new, second specimen of Myxinikela reported here, I reevaluate the soft tissue anatomy and formulate diagnosis for the taxon. Myxinikela has a number of general features of cyclostomes, including cartilaginous branchial baskets, separation between the esophageal and the branchial passages, and a well-differentiated midline finfold. In effect, these features give more lamprey-like appearance to this stem hagfish than previously assumed. Myxinikela still has many traits that set modern hagfishes apart from other vertebrates (e.g., nasohypophyseal aperture, large velar cavity, and cardinal heart) and some intermediate conditions of modern hagfishes (e.g., incipient posterior displacement of branchial region). Thus, Myxinikela provides an important calibration point with which to date origins of these characters.

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