Evolutionary Rates

Evolution is change occurring across generations, that is a gradual accumulation of changes in steps. In order to understand evolution it is essential to characterize that change, and one important component of change is the rate at which that change

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occurs. Understanding the rate of evolution, be it at a molecular or phenotypic level, is therefore a fundamental question in evolutionary biology. These rates are not constant across phylogenetic lineages (BROMHAM and PENNY 2003; KUMAR 2005). For example, evolutionary rates in avian species appear slower than most rates in mammals (MINDELL et al. 1996). Evolutionary rates are affected by different population processes, including selection and genetic drift. When a gene region is selectively neutral, it will accumulate mutations in a clock-like fashion (KIMURA 1983). Within phylogenetics and population genetics, rates of neutral molecular evolution are important parameters allowing researchers to investigate population processes including divergence times, population sizes, etc.

1.6.1 Methods of calculating evolutionary rates

The concept of evolutionary rate is often confused in the literature and may refer to mutation, pedigree or substitution rates (HO and LARSON 2006). Mutation rates typically refer to the rate at which instantaneous changes occur within the genome, excluding lethal or near-lethal mutations (HO and LARSON 2006). They can be estimated by mutant accumulation assays, for example. In these, the rate of change in a fraction of mutants arising from a large mutant-free popualtion is used to calculate the mutation rate (e.g., in Caenorhabditis elegans (DENVER et al. 2000)). Pedigree rates are an estimate of the mutation rate obtained by observing the number of nucleotide changes over a known genealogy of individuals (HO and LARSON 2006).

Substitution rates are difficult to measure directly, so traditionally they have been calculated using calibration methods. In these, the sequence difference among extant taxa is characterized and divided by the age of the most recent common ancestor, calibrated using fossil material or geological data (e.g., (SHIELDS and WILSON 1987). These rates estimate the frequency at which mutations are fixed within a population, as purifying selection or drift acts to remove the majority of changes in the genome. In the case of a perfectly neutral gene region, mutation rates and substitution rates will be the same (KIMURA 1983). Shields and Wilson (1987) utilized this method to estimate the rate of evolution of the mitochondrial genome in birds, using two species

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of geese (Anser and Branta) and found a mean substitution rate of 0.02 s/s/Myr.

(QUINN et al. 1991) estimated a rate of substitution of 0.208 s/s/Myr for the HVR-I of

Branta subspecies based on the divergence between them and the overall mtDNA rate estimated by Shields and Wilson (1987). These rates have been widely used in avian phylogenetics.

Ancient DNA techniques provide an alternative method for estimating substitution rates. Genetic changes can be measured from serially preserved samples. The first study using this technique calculated an evolutionary rate of the hypervariable region

I (HVRI) of the mitochondrial control region, from 344bps of sequence using 96

known age Adélie penguin subfossil bones (LAMBERT et al. 2002). A Bayesian

Markov chain Monte Carlo approach was used, currently implemented in the software

Bayesian Evolutionary Analysis Sampling Trees (BEAST) (DRUMMOND and

RAMBAUT 2007).

1.6.2 Apparent time-dependency of rates

As a result of different approaches to estimating mitochondrial evolutionary and mutation rates, discrepancies between estimates originating from the different methods have become apparent. Rates based on phylogenetic calibrations are lower than those based on serially preserved samples (aDNA), and again, these are substantially lower than mutation rates obtained from pedigree studies and mutant accumulation studies. Neutral theory holds that the rate of mutation (µ) is equal to the

rate of evolution (K) for neutrally evolving sequences (KIMURA 1983). One

hypothesis that has arisen to explain these differences is the “time dependency of molecular rates”. This hypothesis states that the relationship between the age of calibration of a molecular rate (short-term for mutation rates and long-term for phylogenetic rates) and the rate of change can be described by a vertically translated

exponential decay curve (HO et al. 2005). The authors suggest using this curve to

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A heated debate followed. Several studies supported this concept, observing higher rates within or between closely related species compared to more distantly related species (BURRIDGE et al. 2008; GRATTON et al. 2008; HENN et al. 2009; HO et al. 2007; HOWELL et al. 2008). Other studies have criticized the time-dependency hypothesis for not taking into account the methodological upward bias in rate estimation produced by the Bayesian-MCMC approach (BANDELT 2008; DEBRUYNE and POINAR 2009; EMERSON 2007; NAVASCUÉS and EMERSON 2009). A recent study in Adélie penguins sought to address this question within a single species, by estimating a mutation rate following a pedigree approach, and an evolutionary rate from ancient DNA data, for the HVR-I region of the mitochondrial genome (MILLAR et al. 2008a). The pedigree data, from 508 families, was analysed using a model to correct for the effect of heteroplasmies on mutation rate estimation, and gave an estimate of µ=0.55 mutations/site/Myrs, while the ancient DNA approach, using 162 known-age subfossil bones, gave an estimate of K=0.86 substitutions/site/Myrs. These rates were not significantly different and support the assumption of the HVR-I’s neutrality and find no support for the time-dependency hypothesis. However, population genetics theories do predict a time dependent rate at selectively constrained sites due to the removal of slightly deleterious mutations, in contrast to the expectation at neutral sites (no time dependency). Subramanian & Lambert (2011) sought to re-examine the concept of time-dependency by estimating rates separately for neutral and constrained sites in primate mitochondrial genomes. They found no differences between rates calibrated at different evolutionary timescales for synonymous sites; however, an order of magnitude variation at constrained sites was detected. It appears that time-dependency is valid for constrained sites, but not for neutrally evolving regions (SUBRAMANIAN and LAMBERT 2011).