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


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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.

References Alexandrou, M. A. et al., 2013. Genome duplication and multiple evolution origins of complex migratory behaviour in

Salmonidae. Mol. Phylogenet. Evol., Volume 514-23, p. 69.

Arcila, D. et al., 2015. An evalution of fossil tip-dating versus node-age calibration in tetraodontiform fishes (Teleostei:

Percomorphaceae). Mol. Phylogenet. Evol., Volume 82, pp. 131-45.

Ayala, F. J., 1997. Vagaries of the molecular clock. Proc Nat Acad Sci U S A, Volume 94, pp. 7776-83.

Benton, M. J. & Donoghue, P. C. J., 2007. Paleontological evidence to date the Tree of Life. Molecular Biology & Evolution,

24(1), pp. 26-53.

Benton, M. J. & Donoghue, P. C. J., 2007. Paleontological evidence to date the Tree of Life. Mol Biol Evol, Volume 24, pp. 26-

53.

Britten , R. J., 1986. Rates of DNA sequence evolution differ between taxonomic groups. Science, Volume 231, pp. 1393-98.

Brochu, C., 2003. Phylogenetic approaches toward crocodylian history. Earth Planet. Sc. Lett., Volume 31, pp. 357-97.

Brochu, C. A., 2000. Phylogenetic Relationships and Divergence Timing of Crocodylus Based on Morphology and the Fossil

Record. Copeia, 2000(3), pp. 657-73.

Cranston, K. & Rannala, B., 2005. Closing the gap between rocks and clocks. Heredity, Volume 94, pp. 461-2.

Donoghue, P. C. J. & Benton, M. J., 2007. Rocks and clocks: calibratng the Tree of Life using fossils and molecules. Trends in

Ecology and Evolution, Volume 22, pp. 424-31.

Drummond, A. J. et al., 2003. Measurably evolving populations. TREE, Volume 18, pp. 481-88.

Drummond, A. J. et al., 2006. Relaxed Phylogenetics and Dating with Confidence. PLoS Biology, 4(5), p. e88.

Erikson, G. M. et al., 2012. Insights into the ecology and evolutionary success of crocodilians revealed through bite-force and

tooth-pressure experimentation. PLos ONE, 7(3), p. e31781.

Felsenstein, J., 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol, Volume 17, pp.

368-76.

Hasegawa , M. & Kishino , H., 1989. Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian

orders. Jpn J Genet, Volume 64, pp. 243-58.

Holiday, C. M. & Gardner, N. M., 2012. A new eusuchian crocodyliform with novel cranial integument and its significance for the

origin and evolution of Crocodylia. PLoS ONE, 7(1), p. e30471.

Huelsenbeck, J. P. & Ronquist, F., 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, Volume 17, pp.

754-5.

Kimura, M., 1968. Evolutionary rate at the molecular level. Nature, 217(5129), pp. 624-626.

Kumar, S., 2005. Molecular clocks: four decades of evolution. Nat. Rev. Genet., 6(8), pp. 654-62.

Lee, M. S. Y. et al., 2014. Morphological Clocks in Palaeontology and a Mid-Cretaceous Origin of Aves. Syst. Biol., Volume 63,

pp. 442-49.

Lemmon , A. R. et al., 2009. The effect of ambiguous data on phylogenetic estimates obtained by. Syst. Biol., Volume 58, pp.

130-45.

Margoliash, E., 1963. Primary structure and evolution of cytochrome C. Proc. Natl. Acad. Sci. U.S.A., 50(4), pp. 672-9.

Near, T. J. et al., 2014. Phylogenetic relationship and timing of diversification in gonorynchiform fishes inferred using nuclear

gene DNA sequences (Teleostei: Ostariophysi). Mol. Phylogenet. Evo., Volume 297-307, p. 80.

Oaks, J. R., 2011. A time-calibrated species tree of crocodylia reveals a recent radiation of the true crocodiles. Evolution,

65(11), pp. 3285-97.

O'Reilly, J., dos Reis, M. & Donoghue, P. C. J., (in press). Dating tips for divergence time estimation.

Pierce, S. E., 2008. Patterns of Morphospace Occupation and Mechanical Performance in Extant Crocodilian Skulls :A

Combined Geometric Morphometric and Finite Element Modeling Approach. J. Morphol., Volume 269, pp. 840-64.

Pyron, R. A., 2011. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Systematic

Biology , Volume 60, pp. 466-81.

Rambaut, A. & Bromham, L., 1998. Estimating divergence dates from molecular sequences. Mol Biol Evol, Volume 15, pp. 442-

8.

Reisz, R. R. & Muller, J., 2004. Molecular timescales and the fossil record: a paleontological perspective. Trends Genet.,

Volume 20, pp. 237-41.

Ronquist, F. et al., 2012. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera.

Systematic Biology, Volume 61, pp. 973-99.

Runnegar, B., 1982. A molecular-clock date for the origin of the animal phyla. Lethaia, Volume 15, pp. 199-205.

Sanderson, M. J., 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol

Evol, Volume 14, pp. 1218-31.


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Sansom , R. S. & Wills, M. A., 2013. Fossilization causes organisms to appear erroneously primitive by distorting evolutionary

trees. Scientific Reports, Volume 3, p. 5.

Sansom, R. S. et al., 2010. Non-random decay of chordate characters causes bias in fossil. Nature, Volume 463, pp. 797-800.

Schrago, C. G. et al., 2013. Combining fossil and molecular data to date the diversification of New World Primates. J Evolution

Biol, Volume 2438-46, p. 26.

Sharma, P. P. & Giribert, G., 2014. A revised dated phylogeny of the arachnid order Opiliones. Frontiers in Genetics, Volume 5,

p. 255.

Simpson, G. G., 1994. Tempo and Mode in Evolution. s.l.:Columbia University Press.

Slater, G. J., 2013. Phylogenetic evidence for a shift in the mode of mammalian body size at the Ctretaceous-Palaeogene

boundary. Methods in Ecology and Evolution , Volume 4, pp. 734-44.

Thorne , J. L., Kashino, H. & Painter, I. S., 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol

Evol, Volume 15, pp. 1647-57.

Tseng, Z. J. et al., 2014. Himalayan fossils of the oldest known pantherine establish ancient origin of big cats.. Proc. R. Soc. B,

Volume 281.

Wiens, J. J. & Moen, D., 2008. Missing data and the accuracy of Bayesian phylogenetics. J. Syst. Evol., Volume 46, pp. 307-14.

Wiens, J. J. & Morrill, M. C., 2011. Missing data in phylogenetic analysis: reconciling results from. Syst. Biol., Volume 60, pp.

719-31.

Wiens, J. J. & Tiu, J., 2012. Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon

sampling. PloS One, Volume 7, p. e42925.

Wood, H. M. et al., 2014. Treating as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the

palpimanoid spiders. Syst. Biol., Volume 62, pp. 264-284.

Yoder, A. D. & Yang, Z. H., 2000. Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol, Volume 17,

pp. 1081-90.

Zuckerkandl, E. & Pauling, L. B., 1962. Molecular disease, evolution, and genic heterogeneity. In: Horizons in Biochemistry.

New York: Academic Press, pp. 189-225.


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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).


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Fig. 2 Definitions of terms in assigning fossils to clades, showing how minimum and

maximum bounds can be established (Benton & Donoghue 2007)


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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.


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


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Fig. 5 Phylogeny of Crocodylia (Oaks 2011)

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