Lit Review FINAL

Gareth Coleman :: MSci Palaeontology and Evolution :: University of Bristol School of Earth Sciences
Earth Science Research Project :: Literature Review
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Gareth Coleman
MSci Palaeontology and Evolution
University of Bristol School of Earth Sciences
Exploring Calibration in Molecular Clocks: Total Evidence Dating and
the Crocodylian Family Tree
Supervisors: Philip C. J. Donoghue1
, Joseph O’Reilly1
1
University of Bristol School of Earth Sciences
Abstract
The molecular clock is the only viable way to establish an accurate timescale for the evolution of life
on Earth as it can peer through any gaps in an all too incomplete and patchy fossil record. Even so,
the fossil record is still vital in the estimation of divergence times, as it constrains the ranger of
possible age estimates, with fossil remains used as calibration for the molecular clock. The traditional
approach of node-calibration has long been used to calibrate the molecular clock, using the oldest
fossil representative of a clade to establish a minimum age constraint, and inferring a maximum. Due
to the many problems associated with this form of calibration, particularly the arbitrary nature by
which calibration fossils are chosen and the exclusion of fossil data not considered phylogenetically
informative, tip-calibration has been developed, which treats fossils on par with extant taxa, allowing
use of all fossil data and circumnavigating many of these problems. Tip-calibration can be used in
conjunction with the so-called relaxed molecular clock, which accommodates rate variation, and co-
estimation of time and topology, in the form of Total Evidence Dating. However, there are still many
problems associated with tip-calibration, especially the consistently more ancient dates it yields. I
will apply these competing methods to Crocodylia to form a comprehensive tree of the clade and
create models to better alleviate many of the problems still associated with the method.

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Introduction
One of the fundamental goals in evolutionary biology is to establish a timescale for the
evolution of life on Earth in order to seek patterns in, and create models which explain its
diversification, and the factors by which this is influenced. For most of the history of
palaeontology and evolutionary biology, the fossil record has been the sole provider of a
timescale for evolutionary history, as was codified in Simpson’s Tempo and Mode in Evolution
(Simpson, 1994).
In 1962 Zuckerkandl and Pauling proposed the existence of a ‘molecular clock’, based on the
observation that the number of amino acid differences in haemoglobin gene sequences from
different vertebrate lineages changed linearly with time, and asserted that the rate of
evolutionary change of a protein was constant over time and over lineages (Zuckerkandl &
Pauling, 1962). The phenomenon of genetic equidistance was noted by Emanuel Margoliash
in 1963, who recognised that the number of residue differences between cytochrome C of any
two species is proportional to the time elapsed between them since their divergence
(Margoliash, 1963). Both these lines of evidence lead to the formal postulation of the molecular
clock hypothesis in the early 1960s (Kumar, 2005). Later work by Kimura lead to the
development of the neutral theory of molecular evolution, which predicted a molecular clock.
The neutral theory of molecular evolution postulates that, at the molecular level, most
evolutionary changes are caused by random genetic drift of neutral mutant alleles (Kimura,
1968). If most changes during molecular evolution are neutral, then fixations in a population
will accumulate at a rate that is equal to the rate of neutral mutation in an individual, yielding a
clock-like rate (Fig. 1).
However, problems arise in the assumption of clocklike evolution, as in order to infer
divergence dates, a constant rate of evolution throughout the tree must be assumed. Yet much
evidence shows considerable departures from clocklike evolution (Britten , 1986; Ayala, 1997;
Hasegawa & Kishino , 1989) and variation in rate among lineages (Yoder & Yang, 2000). This
lead to the development molecular clock methods that allow independent rates of molecular
evolution in every branch (Drummond et al., 2006). These models allow us to infer phylogenies
(Huelsenbeck & Ronquist, 2001; Felsenstein, 1981), but not to estimate molecular rates or
divergence times due to the inability to separate the individual contributions of rate and time to
molecular evolution. Furthermore, as the rate and time along each branch can only be
estimated as their product, the position of the tree root cannot be estimated without additional
assumptions, such as an out-group. This unrooted alternative to molecular clock was

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suggested by Felsenstein (Felsenstein, 1981) and is the model used in most modern
phylogenetic inference.
More recently, it has become apparent that neither extremes are necessary, and that a relaxed
clock method, which allows for varying rates across the tree, is more affective and is quickly
becoming seen as an affective compromise between strict molecular clock and the unrooted
alternative (Rambaut & Bromham, 1998; Sanderson, 1997; Thorne et al., 1998). However,
there can be significant difficulty in assigning different rates to different lineages, especially
when using large data sets. Relaxed molecular clock models work best when strong prior
hypotheses are used, namely that the rate in a given taxa differs from the rest of the tree (Yoder
& Yang, 2000). Another problem associated with this method is the requirement of a specific
tree topology, as in many cases parts of the tree may be unresolved with multiple possible tree
topologies. Furthermore, the assumption of relaxed molecular clock may alter the posterior
probabilities of alternative tree topologies, so the most optimal tree under a relaxed clock model
may be different from that under the unrooted model or strict molecular clock model. These
problems necessitate an approach where divergence dates and phylogeny are both co-
estimated under a relaxed molecular clock (Cranston & Rannala, 2005).
The fossil record and calibrating the molecular clock
The molecular clock can give divergence time estimates relative to each other, they need
calibrating with fossil evidence to give concrete divergence dates (Benton & Donoghue, 2007).
The traditional way in which this has been done is by node calibration, using fossils to provide
minimum and maximum dates for the time of divergence of a particular lineage. These are
established based on the oldest evidence for the existence of a clade, which is usually the
oldest fossil record of the clade in question. This is often done with a single palaeontological
age estimate which is perceived to be reliable, a common example being the bird-mammal
split. This means that node calibrations require a prior phylogenetic hypothesis (Donoghue &
Benton, 2007).
When using fossils to calibrate nodes, we can give a reasonably definite minimum age or hard
lower bound. This is the oldest known fossil of a group, which tells us that the clade in question
must be of at least that age. When giving a minimum age, we need to be able to determine
both the relative and the absolute dates of the fossils, but more difficult is the necessity to
establish the topology of the tree and whether the fossil is within the crown-group of the clade
of not. Therefore, there may be much disagreement of the minimum age, depending on

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whether particular fossils are considered informative or not. Furthermore, there is a difficulty in
establishing the maximum date, or soft upper bound, as we can never be sure that we have
found the oldest representative of a clade. Instead, we may rely on the lack of fossil evidence
to infer the rough age of the oldest member of a clade (Fig. 2), or statistical models which look
at probability density to estimate the possible upper bounds (Fig. 3), or most commonly, by
using taphonomic controls from the existence of outgroup taxa to interpret evidence of absence
of in-group taxa. We must also establish the prior probability of the time of divergence between
the minimum and maximum age constraints. The resulting probability density functions for
each node calibration are combined with a stochastic branching model to derive induced priors
on non-calibrated nodes in the tree, which enables divergence time estimates for all of the
nodes (Donoghue & Benton, 2007; O'Reilly et al., (in press)).
There are many problems associated with node-calibration. If the fossil is to be considered
phylogenetically informative, we must be certain of its phylogenetic positioning. This excludes
much fossil data which is less well preserved and often fragmentary, and therefore may be of
uncertain phylogenetic affinity. Older fossils are therefore often ignored for younger and more
complete fossils which can be more readily assigned to the clade in question. However, not
only does this leave out a lot of potential data, it also leads to inaccurate calibrations, as it
gives a skewed view of the phylogeny of a clade by not including certain species, and missing
part of its evolutionary history. Also, maximum age constraints based on the absences of
fossils or statistical models are not considered acceptable by many researchers, as well as the
often random and arbitrary nature of the choices of competing parameters and potential fossils
for calibration, which can vastly affect the outcome. Finally, the node calibrations are invariably
transformed in the establishment of the joint time prior, to the extent that they often have little
relation to the original fossil evidence (Donoghue & Benton, 2007; O'Reilly et al., (in press)).
Tip-calibration
A more recent method of calibration is fossil tip calibration, a method requiring both molecular
sequence data and morphological character datasets, analysed using molecular and
morphological models of evolution (Pyron, 2011; Ronquist et al., 2012). One important
innovation of this method is that it allows fossil species data to be incorporated into divergence
time analyses on par with extant taxa, being included as distinct taxa, similar to living taxa,
rather than merely constraining the prior probability of the clade age. Fossils of known age
calibrate evolutionary rate based on their phylogenetic position, branch length, and an inferred
rate of evolution. Tree topology can be estimated independently or co-estimated with

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divergence time analysis, with evolutionary rate based on either independent or correlated
rates of morphological and molecular evolution. As calibrations no longer serve as prior
estimates of clade age, tip calibration therefore provides a way to circumnavigate many of the
problems associated with node-calibration, such as the limited fossil data that can be used,
and arbitrary decisions about whether or not a fossil is phylogenetically informative. Tip
calibrations also summarise the age of single species, which avoids over-interpretation of
negative evidence in the establishment of maximum constraints (O'Reilly et al., (in press)).
There are problems associated with tip-calibration, namely the dating of the fossil tips. Almost
all total evidence dating studies had used point age-estimates for fossil species used in tip-
calibration, based on the assumption that the age of the fossil is definitely known. This is
sometimes justified as acceptable by some who claim that resulting errors are negligible
(Ronquist et al., 2012; Sharma & Giribert, 2014). However, it is well documented that the age
of a fossil can never be known without a degree of uncertainty, and there are in fact often large
degrees of uncertainty, which must be taken into account for both node- and tip-dating. The
age can therefore only be constrained within minimum and maximum bounds, the span of
which depends on the evidence available, and therefore presenting many of the same
problems faced by node-calibration. While node-calibrations may rely primarily on the earliest
fossil which can be confidently assigned to the clade in question for a minimum date, with a
maximum implied through negative evidence (Benton & Donoghue, 2007; Reisz & Muller,
2004) (Fig. 2), tip-calibration requires at the least the establishment of minimum and maximum
ages. Many of the techniques and models used in node-calibration can therefore be applied to
the data of fossil taxa in tip-dating. There is a further peculiarity associated with tip-calibrations
in relation to fossil ages. Particularly, many species used for calibration will occur through a
stratigraphic range, rather than being one off occurrences. This has little bearing on node-
calibration, as it is the oldest fossil occurrence that is relevant, but has far more relevance in
tip-calibration. As by the morphological species definition, there will be little or no
morphological variation in such species, this data must therefore be incorporated into the age
uncertainty that is associated with that particular fossil taxon. It is therefore likely that
uncertainty in tip-calibration will exceed that of node-calibration.
Total Evidence Dating
Tip-calibration can also be used in Total-Evidence Dating (TED). TED is a combination of
approaches which include the relaxed morphological clock, tip-calibration and co-estimation of
time and topology (O'Reilly et al., (in press)). These methods can all be used individually in

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order to augment a conventional molecular clock analysis, which may avoid the problematic
assumption that molecular and morphological data co-vary, following a single rate model
(Schrago et al., 2013). It is possible to co-estimate time and topology using dated tips and
morphological data without any molecular data, as was done by Lee et al. in their analysis of
body size evolution through the dinosaur-bird evolutionary transition (Lee et al., 2014). This
approach can be adopted in order to obtain clade ages for extinct clades, rather than minimum
ages. Tip-calibration also allows the combination of both DNA and morphological data, which
may facilitate more accurate estimates of evolutionary rate, as well as the inclusion of fossils
which would otherwise not be included due to uncertainty of their phylogenetic position, as it
is able to co-estimate time and topology.
Although originally applied to divergence time analyses of amphibians (Drummond et al., 2003)
and insects (Ronquist et al., 2012), TED has been applied to a variety of different clades
(Slater, 2013; Schrago et al., 2013; Tseng et al., 2014; Near et al., 2014; Alexandrou et al.,
2013; Arcila et al., 2015; Wood et al., 2014; Sharma & Giribert, 2014), including entirely extinct
clades which rely entirely on morphological data (Lee et al., 2014). TED was initially seen as
being advantageous due to it being less sensitive to root time prior densities and yielding
divergence times with more precision than node-calibration (Ronquist et al., 2012). However,
many studies have shown that tip calibration is often more sensitive to root time prior densities
and yield less precise divergence times. It also routinely yields older age estimates than node-
calibration (Ronquist et al., 2012; Slater, 2013; Schrago et al., 2013; Tseng et al., 2014; Arcila
et al., 2015; Wood et al., 2014; Sharma & Giribert, 2014).
Another problem with TED lies in the co-estimation of time and topology. Combined with
current methods of tip-calibration, it would allow fossil ages to constrain their phylogenetic
position and effect the tree topology and impact the estimation of rates and dates. This follows
the historical tradition in palaeontology to assume that the age of fossil species reflect their
phylogenetic position, which has now be abandoned in favour of phylogenetic based on
phenotype, which can be refined by stratigraphy. This change reflects the acknowledgement
that age does not necessarily inform topology. However, this is problematic if time and topology
co-estimation continues to allow fossil ages to inform topology. This can be avoided by
independent analysis of topology before divergence time estimation. Though it is unfortunate
that this stops the integration of phylogenetic uncertainty into divergence time estimation,
resolving phylogenetic uncertainty using tip age is not acceptable with current methods
(O'Reilly et al., (in press)).

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It is important to note that TED and node-calibration are not mutually exclusive. Some temporal
constraints are more suited to be implemented by node-calibration, and some fossil-evidence
is better reflected as node-calibrations, rather than as component fossils of species in tip-
calibrations. Node- and tip-calibrations can be used concurrently, with node-calibrations
serving to alleviate, to some extent, the tendency of tip-calibration to yield unacceptably old
divergence dates, as it places additional constraints on the ages of internal nodes of a tree.
This requires a fixed tree topology, and therefore does not allow for topology and time to be
co-estimated, although this is not necessarily a problem given the problems associated with
topology and time co-estimation stated above (Ronquist et al., 2012; O'Reilly et al., (in press)).
A big problem facing TED, and indeed a problem pervasive in all areas of palaeontology, is
the incompleteness of the fossil record. The impact of missing data on Bayesian phylogenetic
topology estimation has been investigated, with the majority of studies suggesting that there
is unlikely to be a large negative impact (Wiens & Morrill, 2011; Wiens & Moen, 2008; Wiens
& Tiu, 2012; Lemmon et al., 2009), except where there is a comparatively small number of
non-missing sites (Wiens & Moen, 2008). However, this is a problem for topology based on
morphological data due to the comparatively small datasets when compared to molecular
sequence alignments. These problems are further aggravated when we consider that non-
random nature of the missing morphological data, where fossil data are biased towards the
preservation of hard, mineralised structures. When there is exceptional preservation of soft-
tissue, the fossil data may be subject ‘stem-ward slippage’, where features are lost to decay in
reverse phylogenetic order, giving the fossil the appearance of a more primitive evolutionary
grade (Sansom & Wills, 2013; Sansom et al., 2010). The effects of missing data can be
minimised by using sub-sampling approaches (Pyron, 2011; Ronquist et al., 2012), or models
of fossilisation employed to account for the loss of characters during perseveration. However,
these approaches may not be realistic solutions to the problems due to the taxonomic variation
in preservation.
It is also important to mention that the morphological data used in these analyses can be either
continuous or discrete. Discrete morphological data, in the form of data matrices showing the
absence and presence of a number of characters, have long been used in the field of cladistics
and has been used in TED analyses. Continuous data, derived from the landmarking of
specimens, have not been used in these analyses. Continuous data may be more easily
modelled, however, there it is not certain how well analyses incorporating them will run, or how

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easily the data continuous data can be integrated with discrete data. It is also unsure whether
tip-calibration will ultimate give more accurate divergence estimates that node-calibrations,
and whether it is advisable to use co-estimation of time and topology.
Crocodilians and future research
Crocodilians are an interesting group to study, due to the availability of molecular data for all
extant species, as well as their extensive fossil record. While the fossil record for the clade is
rich, comprising of around 160 fossil species, there are only 23 extant species. Within the
extant crocodilians, there are three families, Alligatoridae, Crocodylidae and Gavialidae.
Crocodylus is the most widely distributed, ecologically diverse and species rich genus. There
has been much debate into the internal topology of the clade, particularly the positioning of the
Gavialidae. The traditional topology groups Alligatoridae and Crocodylidae together in the
clade Brevirostres, with Gavialidae as a sister-group (Holiday & Gardner, 2012; Brochu, 2003)
(Fig. 4). More recent research has given a different topology, with Gavialidae and Crocodylidae
shown to form a monophyletic group with Alligatoridae as a sister group (Erikson et al., 2012)
(Fig. 5). There has also been much debate about the divergence times of the clades within
Crocdylia, with many studies traditional placing the origin of Crocodylus in the Cteaceous,
while more recent research has suggested a more recent origin of the genus in the Late
Miocene (Oaks, 2011).
In my study, I intend to carry out analyses to test whether or not tip-calibration is more reliable
and accurate in comparison to node-calibration and whether it is advisable to co-estimate time
and topology. I also plan to test if continuous data performs better that discrete data, and
whether it can be integrated with discrete morphological data and molecular data, or not. I shall
use morphological and molecular data for all 23 extant species, as well as morphological data
for 44 extinct species. The morphological data matrix shall be taken from Brochu (2000) and
the molecular data from Oaks (2011). I shall also use continuous data of extant species from
Pierce (2008), and collect continuous data of fossil species from the literature. I shall also use
the literature to data all of the fossil species. The analyses can be carried out in mcmctree or
mrBase.
Concluding remarks
Due to these problems, it seems that there is little evidence for the superiority of tip-calibration
over node-calibration. However, the advantages of tip-calibration are primarily that it relies on
fewer assumptions compared node-calibration, as well as the ability to incorporate potentially

9
all fossil data, and the incorporation of both molecular and morphological data. In combination
with other approaches, it provides many inherent advances. This make TED an exciting and
promising area of research, encompassing a variety powerful methods and tools, particularly
as we develop evolutionary models, protocols for dating fossils and accounting for missing
data. Most importantly, TED provides a powerful framework for the incorporation and
unification of palaeontological and molecular data, and testing the performance of new types
of data, such as continuous morphological data, in establishing evolutionary timescales.
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Fig. 1 Graph demonstrating principle of molecular clock, showing the linear relation between
number of substitution and time (Zuckerkandl and Pauling 1962).

12
Fig. 2 Definitions of terms in assigning fossils to clades, showing how minimum and
maximum bounds can be established (Benton & Donoghue 2007)

13
Fig. 3 Two patterns for the distribution of probabilities between minimum and maximum
constraints on a clade’s origin data (a). (b) shows a logistic curve and (c) an assumption
added that there may be older fossils with less certain affinity.

14
Fig. 4 Phylogeny of Crocodylia (Holiday and Gardner 2012).

15
Fig. 5 Phylogeny of Crocodylia (Oaks 2011)

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