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Evolution & Extinction /
The Molecular Clock and/or/versus the Fossil Record
Y. Asar et al. (2022):
Evaluating
the accuracy of methods for detecting correlated rates of molecular and morphological evolution. In PDF,
bioRxiv.
See also
here.
!
Note figure 1 (on PDF-page 9): A flowchart of simulation study. About molecular and morphological phylograms,
morphological characters and sequence alignments.
F.J.Ayala (1999):
Molecular
clock mirages. Abstract,
BioEssays, 21: 71–75.
"... The hypothesis of the molecular clock proposes that molecular evolution occurs at rates
that persist through time and across lineages, for a given gene.
[...]
Four recent papers show that none of the predictive hypotheses that have been proposed
can be generally maintained. The conclusion is that molecular evolution is dependent
on the fickle process of natural selection. But it is a time-dependent process, so that
accumulation of empirical data often yields an approximate clock, as a consequence of the
expected convergence of large numbers. ..."
F.J.Ayala (1997):
Vagaries
of the molecular clock. Free access,
Proc. Natl. Acad. Sci. USA, 94: 7776-7783.
"... The hypothesis of the molecular evolutionary clock asserts that informational
macromolecules (i.e., proteins and nucleic acids) evolve at rates that are constant through
time and for different lineages. The clock hypothesis
has been extremely powerful for determining evolutionary
events of the remote past for which the fossil and other
evidence is lacking or insufficient. ..."
! C. Beimforde et al. (2014): Estimating the Phanerozoic history of the Ascomycota lineages: combining fossil and molecular data. In PDF, Molecular Phylogenetics and Evolution, 78: 386-398. See also here.
! M.J. Benton et al. (2009): Calibrating and constraining the molecular clock. PDF file, In: S.B. Hedges and S. Kumar (eds.): The Timetree of Life (see here).
!
M.J. Benton and B.C. Emerson (2007):
How
did life become so diverse? The dynamics of diversification according to the fossil record and
molecular phylogenetics. Open access, Palaeontology, 50: 23-40.
Note text figure 1: Patterns of diversification of: A, families of marine invertebrates;
B, species of vascular land plants; C, families of
non-marine tetrapods; and D, families of insects.
! M.J. Benton and P.C.J. Donoghue (2007): Paleontological Evidence to Date the Tree of Life. In PDF. See also here. Molecular biology and evolution.
Michael Benton, Department of Earth Sciences, University of Bristol, UK: Accuracy of Fossils and Dating Methods (an ActionBioscience.org original interview, American Institute of Biological Sciences).
M.J. Benton and P.N. Pearson (2001): Speciation in the fossil record. PDF file, Trends in Ecology and Evolution, 16.
M.J. Benton et al. 2000):
Quality of the fossil record through time.
Nature, 403: 534-537.
See also
here.
"... new assessment methods, in which the order of fossils in the rocks
(stratigraphy) is compared with the order inherent in evolutionary
trees (phylogeny), provide a more convincing analytical tool:
stratigraphy and phylogeny offer independent data on history. ..."
S. Bonneville et al. (2020): Molecular identification of fungi microfossils in a Neoproterozoic shale rock. In PDF, Science Advances, 6: eaax7599.
Brent H. Breithaupt (1992):
The use of fossils
in interpreting past environments.
PDF file, Pages 147–158, in:
Tested studies for laboratory teaching, Volume 13 (C. A. Goldman, Editor). Proceedings of the 13th
Workshop/Conference of the Association for Biology Laboratory Education.
This expired link is now available through the Internet Archive´s
Wayback Machine.
!
L. Bromham and D. Penny (2003):&xnbsp;
The
modern molecular clock.
Nature Reviews Genetics, 4: 216–224.
See also
here.
"... The evolutionary dates measured by molecular
clocks have been controversial, particularly if they clash
with estimates taken from more traditional sources such
as the fossil record.
[...] The molecular clock — a relatively constant rate of
accumulation of molecular differences between
species — was an unexpected discovery that has provided
a window on the mechanisms that drive molecular
evolution. ..."
G.E. Budd and S. Jensen (2020):
A
critical reappraisal of the fossil record of the bilaterian phyla. Abstract,
Biological Reviews, 75_253-295.
"... Indeed, the combination of the body and trace fossil record demonstrates a
progressive diversification through the end of the Proterozoic well into the Cambrian
and beyond, a picture consistent with body plans being assembled during this time. ..."
G.E. Budd (2008): The earliest fossil record of the animals and its significance. Phil. Trans. R. Soc. B, 363: 1425–1434. See here.
R.J. Burnham (2008): Hide and Go Seek: What Does Presence Mean in the Fossil Record. Abstract, Annals of the Missouri Botanical Garden, 95: 51-71. See also here (in PDF).
!
C. Cai et al. (2022):
Integrated
phylogenomics and fossil data illuminate the evolution of beetles. Open access,
R. Soc. Open Sci. 9:
211771.
Note figure 2: Timescale of beetle evolution displayed as a family-level tree.
!
"... Our divergence time analyses recovered
a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders
and a Triassic–Jurassic origin of most extant families, while fundamental divergences within beetle
phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution ..."
E. Callaway (2015): Computers read the fossil record. Palaeontologists hope that software can construct fossil databases directly from research papers. In PDF, Nature Toolbox. See also here.
!
J.T. Clarke et al. (2011):
Establishing
a time-scale for plant evolution. PDF file,
New Phytologist. See also
here.
!
Note figure 2: A representative tree of relationships between model representatives
of the major land plant lineages whose plastid or nuclear genomes
have been fully sequenced.
Figure 7: Chronogram for land plant evolution.
Figure 8: Chronograms for the six molecular clock analyses conducted.
"... We reject both a post-Jurassic origin of angiosperms and a post-Cambrian origin
of land plants. Our analyses also suggest that the establishment of the major
embryophyte lineages occurred at a much slower tempo than suggested in most
previous studies. ..."
!
M. Coiro et al. (2019):
How
deep is the conflict between molecular and fossil evidence on the age of angiosperms?
Free access,
New Phytologist, doi: 10.1111/nph.15708.
"... Critical scrutiny shows that supposed pre-Cretaceous angiosperms either represent
other plant groups or lack features that might confidently assign them to
the angiosperms. ..."
! F.L. Condamine et al. (2013): Macroevolutionary perspectives to environmental change. In PDF, Ecology letters.
!
J.A. Cunningham et al. (2016):
The
origin of animals: can molecular clocks and the fossil record be reconciled?
Open access, Bioessays, 39. See also
here
(in PDF).
Note figure 1: Summary of major Ediacaran and early Cambrian fossil assemblages.
!
Figure 2. The mismatch between the fossil and molecular clock
records of early animal evolution.
"... Molecular clocks estimate that animals originated and began diversifying over 100 million years
before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection
reveals that clock estimates and the fossil record are less divergent than is often claimed.
[...] A considerable discrepancy remains, but much of this can be explained by the limited
preservation potential of early metazoans and the difficulties associated with their identification
in the fossil record.
!
M. Dohrmann and G. Wörheide (2017):
Dating
early animal evolution using phylogenomic data. Open access,
Scientific reports, 7.
!
Note Figure 4: Time-calibrated phylogeny of animals.
! P.C.J. Donoghue and Z. Yang (2016): The evolution of methods for establishing evolutionary timescales. In PDF, Phil. Trans. R. Soc., B 371.See also here (abstract).
P.C.J. Donoghue and M.J. Benton (2007): Rocks and clocks: calibrating the Tree of Life using fossils and molecules. In PDF, Trends in Ecology and Evolution.
A. Dornburg et al. (2011):
Integrating
Fossil Preservation Biases in the Selection of Calibrations for Molecular
Divergence Time Estimation. PDF file,
Syst. Biol., 60: 519-527.
Website saved by the Internet Archive´s
Wayback Machine.
M. dos Reis et al. (2015): Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Free access, Current Biology, 25: 2939–2950.
E.J.P. Douzery et al. (2004):
The
timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?. Free access,
Proceedings of the National Academy of Sciences, USA, 101: 15386–15391.
Note figure 1: Divergence time estimates (Mya) among eukaryotes.
White rectangles delimit95%credibility intervals on node ages. Stars indicate the
six nodes under prior paleontological calibration.
!
"... We show that, according to 95% credibility intervals, the eukaryotic
kingdoms diversified 950–1,259 million years ago (Mya), animals
diverged from choanoflagellates 761–957 Mya,
[...] Interestingly, these relaxed clock time estimates are
much more recent than those obtained under the assumption of a
global molecular clock, yet bilaterian diversification appears to be
~100 million years more ancient than the Cambrian boundary. ..."
!
A.J. Drummond et al. (2006):
Relaxed
phylogenetics and dating with confidence. Open access,
PLoS Biol 4: e88. DOI: 10.1371/journal.pbio.0040088.
"... In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a
continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and
that the real evolutionary process lies between these two extremes.
Fortunately, intermediate models employing
relaxed molecular clocks have been described. ..."
!
F. Forrest (2009):
Calibrating
the Tree of Life: fossils, molecules and evolutionary timescales. Free access,
Annals of Botany, 104: 789–794.
"... New methods have now been proposed
to resolve potential sources of error associated with the calibration
of phylogenetic trees, particularly those involving
use of the fossil record.
[...] ! "...the fossil record remains the most reliable source of information
for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken
into account. ..."
!
P.G. Gensel (2021):
When
did terrestrial plants arise? Abstract,
Science, 373: : 736-737.
"... There has been a discrepancy in the time of land plant origination between
molecular clock estimations (based on genes and RNA) and fossil record estimates
(based on morphology). On page 792 of this issue, Strother and Foster (6) describe
fossilized spores whose characteristics raise the possibility that land plants arose
by co-opting algal genes, along with acquiring de novo genes, and that the former
would account for the molecular clock predating the fossil record. ..."
!
D.E. Greenwalt (2023); Paleobiology Department at the Smithsonian’s National Museum of Natural History:
Remnants
of Ancient Life: The New Science of Old Fossils. Google books.
See also
here.
"... We used to think of fossils as being composed of nothing but rock and minerals, all
molecular traces of life having vanished long ago. We were wrong. Remnants of Ancient Life
reveals how the new science of ancient biomolecules — pigments, proteins, and DNA that
once functioned in living organisms tens of millions
of years ago — is opening a new window onto the evolution of life on Earth. ..."
S. Guindon (2020):
Rates
and Rocks: Strengths and Weaknesses of Molecular Dating Methods. Open access,
Frontiers in Genetics, 11.
"... molecular dating will undoubtedly keep playing
a crucial role in biology in the future. Our understanding of
important phenomena such as species diversification or dispersal,
population migration and demography, or the molecular
signature resulting from environmental changes, depends on our
ability to date past evolutionary events. The wealth of available
techniques to perform this task provides a powerful set of tools
to make progress in this direction. ..."
!
S.B. Hedges (2009):
Life. PDF file,
In: S.B. Hedges and S. Kumar (eds.): The Timetree of Life.
!
See here.
These expired links are now available through the Internet Archive´s
Wayback Machine.
! J.B. Hedges (2004): A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC evolutionary biology.
S.Y.W. Ho (2020): The molecular clock and evolutionary rates across the tree of life. Abstract. In: S.Y.W. Ho (ed.): The molecular evolutionary clock. Springer International Publishing, 3–23.
!
S.Y.W. Ho and S. Duchêne (2014):
Molecular-clock
methods for estimating evolutionary
rates and timescales. Free access,
Molecular ecology, 23: 5947–5965.
"... The molecular clock presents a means of estimating evolutionary rates and timescales
using genetic data.
[...] We provide an outline of the various clock methods and models that are available,
including the strict clock, local clocks, discrete clocks and relaxed clocks. Techniques
for calibration and clock-model selection are also described, along with methods for
handling multilocus data sets.
M.J. Hopkins et al. (2018):
The
inseparability of sampling and time and its influence on attempts to
unify the molecular and fossil records. Free access,
Paleobiology, 44: 561–574.
"... Although neither the molecular record nor the
fossil record are perfect, the two records bear
independent limitations, and what is missing
from one is often available in the other. We
must deal with the different and sometimes
complex relationships between time and sampling
to take full advantage of the complementary
nature of the two records. ..."
M. Kearney (2002): Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. PDF file, Systematic biology, 51: 369-381.
! S.M. Kidwell and S.M. Holland (2002): The Quality of the Fossil Record: Implications for Evolutionary Analyses. PDF file, Annual Review of Ecology and Systematics, 33: 561-588. See also here.
Susan M. Kidwell and Karl W. Flessa: THE QUALITY OF THE FOSSIL RECORD: Populations, Species, and Communities.- Annu. Rev. Earth Planet. Sci. 1996 24: 433-464. Full Online Access via Annual Reviews, Go to Annual Reviews Search Page (Biomedical Sciences), Search for "Kidwell" (Field Author, Last Name).
M. Kowalewski and R.K. Bambach (2008): The limits of paleontological resolution. In PDF, High-resolution approaches in stratigraphic paleontology. This expired link is available through the Internet Archive´s Wayback Machine.
!
S. Kumar&xnbsp;(2005):
Molecular
clocks: four decades of evolution. Open access,
Nature Reviews Genetics, 6: 654–662.
Don't miss the Timeline: Four decades of molecular clocks.
! Michel Laurin (2012): Recent progress in paleontological methods for dating the Tree of Life. In PDF, Frontiers in Genetics, 3.
M.S.Y. Lee and S.Y.W. Ho (2016):
Molecular
clocks.
Current biology, 26: R399-R402.
See also
here.
Note figure 3:
Divergence dates derived from molecular clocks are often older than those suggested
by the fossil record.
!
R. López-Antoñanzas et al. (2022):
Integrative
Phylogenetics: Tools for
Palaeontologists to Explore the Tree
of Life. Open access, Biology, 11: 1185.
https://doi.org/10.3390/
biology11081185.
"... The statistical techniques mentioned above have only begun to be applied to questions
in palaeontology over the past decade but have found extensive applications in
phylogenetic comparative analysis, quantitative genetics, and ecology. Complementary
methodologies that combine morphological and molecular approaches can provide novel
answers to broad evolutionary and deep-time questions ..."
! S Magallón et al. (2013): Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates. Free access, American Journal of Botany, 100: 556-573.
G.J. Morgan (1998):
Emile
Zuckerkandl, Linus Pauling, and the molecular evolutionary clock, 1959-1965. In PDF,
Journal of the History of Biology, 31: 155-178.
See also
here.
H. Morlon et al. (2011): Reconciling molecular phylogenies with the fossil record. In PDF, PNAS, 108: 16327-16332.
! J.L. Morris et al. (2018): The timescale of early land plant evolution. In PDF, PNAS, 115. See also here.! NATURE, Nature Debates: Andrew Smith, Department of Palaeontology, the Natural History Museum, London: Is the fossil record adequate? This debate introduces the topic and the conflicting viewpoints that surround it.
!
Y. Nie et al. (2020):
Accounting
for uncertainty in the evolutionary timescale of green plants through clock-partitioning and
fossil calibration strategies. In PDF, Syst. Biol., 69: 1–16.
See also here.
!
Note figure 5: Time-tree of green plants.
!
"... By taking into account various sources of uncertainty, we
estimate that crown-group green plants originated in the
Paleoproterozoic–Mesoproterozoic (1679.7–1025.6 Ma),
crown-group Chlorophyta and Streptophyta originated
in the Mesoproterozoic–Neoproterozoic (1480.0–902.9
Ma and 1571.8–940.9 Ma), and crown-group land plants
originated in the Ediacaran to middle Ordovician (559.3–
459.9 Ma). ..."
K.J. Niklas and B.H. Tiffney (2022):
Viridiplantae
Body Plans Viewed Through the Lens of the Fossil Record and Molecular Biology. Open access,
Integrative and Comparative Biology,
"... A review of the fossil record coupled with insights gained from molecular and developmental biology
reveal a series of body plan transformations that gave rise to the first land plants.
Across diverse algal clades, including the green algae and their descendants, the plant body plan underwent
a unicellular -- colonial -- simple multicellular -- complex multicellular transformation series. ..."
Note figure 4: Scenarios for the evolution of the first land plant sporophyte
resulting from delayed zygotic meiosis.
J.H. Nitta et al. (2022): An open and continuously updated fern tree of life. Free access, Front. Plant Sci., 13: 909768. doi: 10.3389/fpls.2022.909768.
Geobiology,
Department of Earth Sciences,
Oxford University:
Questioning
the evidence for Earth's oldest fossils.
Now provided by the Internet Archive´s Wayback Machine.
!
Palaeontologia Electronica:
Fossil
Calibration Database.
The Fossil Calibration Database is a curated collection of well-justified calibrations.
They also promote best practices for justifying fossil calibrations and citing calibrations
properly. Raising the Standard in Fossil Calibration! See also:
D.T. Ksepka et al. (2015):
The
Fossil Calibration Database, A New Resource for Divergence Dating. Abstract,
Systematic Biology.
J.F. Parham et al. (2012): Best Practices for Justifying Fossil Calibrations. In PDF, Syst Biol., 61: 346-359. See also here (abstract). Darwin's theory of evolution; evolution as a mechanism for change; the nature of species; the nature of theory; paleontology, geology, and evolution; and determining the age of fossils and rocks. The Online booklet contains straightforward definitions as well as discussions of complex ideas. Navigate using the left-hand toolbar. There is also a PDF printable version available.
S.M. Porter (2004):
The
fossil record of early eukaryotic diversification. In PDF,
Paleontological Society Papers, 10: 35-50.
Still available via Internet Archive Wayback Machine.
See also
here.
Note figure 1: A current view of eukaryote phylogeny, based on a consensus of molecular and
ultrastructural data.
K.M. Pryer et al. (2004): Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences. Open access, American Journal of Botany, 91: 1582-1598.
!
T.B. Quental and C.R. Marshall (2010):
Diversity
dynamics: molecular phylogenies need the fossil record. In PDF,
Trends in ecology & evolution,
25: 434-441.
See also
here.
"... It appears that molecular phylogenies can tell us
only when there have been changes in diversification
rates, but are blind to the true diversity trajectories and
rates of origination and extinction that have led to the
species that are alive today. ..."
R.R. Reisz and J. Müller (2004): Molecular timescales and the fossil record: a paleontological perspective. In PDF, Trends in Genetics.
D.L. Rabosky (2014): Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees. PLoS ONE, 9: e89543. doi:10.1371/journal.pone.0089543
S.S. Renner (2005):
Relaxed
molecular clocks for dating historical plant dispersal events. In PDF,
Trends in plant science, 10: 550-558.
See also
here.
!
A. Rojas et al: (2021):
A
multiscale view of the Phanerozoic fossil record reveals the three major
biotic transitions. Open access,
Communications Biology, 4.
"... we demonstrate that Phanerozoic oceans
sequentially harbored four global benthic mega-assemblages. Shifts in dominance patterns
among these global marine mega-assemblages were abrupt (end-Cambrian 494 Ma; end-
Permian 252 Ma) or protracted (mid-Cretaceous 129 Ma), and represent the three major
biotic transitions in Earth’s history. ..."
! D. Silvestro et al. (2015): Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record. In PDF, New Phytologist, 207: 425-436.
!
C. Strullu-Derrien et al. (2018):
The
origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. Free access,
New Phytologist, 220: 1012–1030.
!
Note figure 1: Geological timescale with oldest known
fossils. Left: Antiquity of genomic traits related
to mycorrhizal evolution based on
molecular clock estimates. Right: Oldest known fossils.
Figure 5: Simplified phylogenetic tree showing the minimum stratigraphic ranges
of selected groups based on fossils (thick bars) and their minimum implied range
extensions (thin lines).
D. Su et al. (2022):
Large-scale
phylogenomic analyses reveal the monophyly of bryophytes and neoproterozoic origin of land plants
Open access, Molecular Biology and Evolution, 38: 3332–3344.
!
Note figure 1: The concatenation species tree of land plants and their algal relatives.
!
Figure 2: The coalescent species tree of land plants and their algal relatives.
"... We found that studies favoring a Neoproterozoic origin of land plants (980–682 Ma) are informed more by
molecular data whereas those favoring a Phanerozoic origin (518–500 Ma) are informed more by
fossil constraints. Our divergence time analyses highlighted the important contribution
of the molecular data (time-dependent molecular change) when faced with contentious fossil evidence.
[..] A careful
integration of fossil and molecular evidence will revolutionize
our understanding of how land plants evolved.
Teaching Biology, Random Posts on Biological Topics (by Marc Srour, Enalia Physis Environmental Research Center, Cyprus): Taxonomic Bias in the Fossil Record: Is it really an issue?
!
A.M.F. Tomescu (2021):
Mysteries
of the bryophyte–tracheophyte transition revealed: enter the eophytes. Free access,
New Phytologist,
Note fig. 1: Timeline and evolutionary hypothesis for early land plants.
Worth checking out:
!
D. Edwards et al. 2022a):
Piecing
together the eophytes–a new group of ancient plants containing cryptospores. Free access,
New Phytologist, 233: 1440–1455.
!
D. Edwards et al. 2022b):
Earliest
record of transfer cells in Lower Devonian plants. Free access,
New Phytologist, 233: 1456–1465.
M.J. Watson and D.M. Watson (2020): Post-Anthropocene Conservation. Open access, Trends in Ecology & Evolution.
!
C.H. Wellmann et al. (2023).
Terrestrialization
in the Ordovician. Open access,
Geological Society, London, Special Publications, 532.
"... This contribution reviews the evidence for terrestrial organisms during the Ordovician (microbial,
land plant, fungal, animal)
[...] We conclude that the Ordovician was a critical period during the
terrestrialization of planet Earth that witnessed the transition from a microbial terrestrial biota to one dominated
by a vegetation of the most basal land plants. ..."
Wikipedia, the free encyclopedia:
Timeline
of the evolutionary history of life.
!
Molecular clock.
!
Molekulare Uhr (in German).
DNA sequencing.
DNA-Sequenzierung (in German).
N. Wikström et al. (2022): No phylogenomic support for a Cenozoic origin of the “living fossil” Isoetes. OPen access, American Journal of Botany.
A.C. Wilson et al. (1987): Molecular time scale for evolution. Abstract, Trends in Genetics, Trends in Genetics Volume 3: 241-247.
!
A.C. Wilson (1985):
The
molecular basis of evolution. In PDF,
Scientific American, 253: 164-175.
See also
here.
!
H.S. Yoon et al. (2004):
A
molecular timeline for the origin of photosynthetic eukaryotes.
PDF file, Mol. Biol. Evol., 21: 809-818.
See also
here.
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