testing for heterogeneity in rates of morphological evolution: discrete character change in the...
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![Page 1: Testing for heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi)](https://reader034.vdocument.in/reader034/viewer/2022051815/53ff8eae8d7f7261088b4636/html5/thumbnails/1.jpg)
Testing for heterogeneity in rates of morphological evolution: discrete
character change in the evolution of lungfish (Sarcopterygii; Dipnoi)
Steve C.Wang
Graeme T.Lloyd
Stephen L.Brusatte
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• Has several meanings and can be taxic- or character-based
• Can inform us about the mode of evolution• Critical to understanding macroevolutioanry
dynamics (e.g. punk eek)
Rates of evolution
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Discrete character rates: a brief history
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Discrete character rates: a brief historyDerstler 1982 Forey 1988
Ruta et al. 2006 Brusatte et al. 2008
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Problems with previous methodsPhyletic or phylogenetic:
Zero duration branch problem:
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Problems with previous methods
• Still to be addressed:– Uncertainty over dating– Phylogenetic uncertainty– Uncertainty over character optimisation– Distribution of rates across tree and not
just time– Lack of a significance test/null hypothesis
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Some solutions
• Dating approach (Ruta et al./Brusatte et al.)• Randomising dates (accuracy vs. precision)• Multiple optimisations (ACCTRAN/DELTRAN)• Examining multiple MPTs• Patristic dissimilarity (Wagner 1997)
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Data set
• Chose lungfish for initial study as thought to have a marked difference in rates between early Devonian and post-Devonian
• We use a supermatrix that contains representatives of most known genera and spans their entire history
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Method 1 - Changes over time
• Problem of branches is they have a time span, where do we bin them if this crosses two time bins?
• Alternative approach (Chaloner & Sheerin 1979) is to ask when changes occur
• We don’t know precisely, but we do have the bounds of the branch duration
• We can thus select random ages for each character change along a branch between its beginning and end
• Repeating 1,000 times can give us a measure of accuracy as a confidence interval
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Method 1 - Changes over time
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Method 2 - Randomisation branch test
• But we are also interested in where rates are distributed across the tree
• A simple way of looking at this is to ask which branches show a significant excursion from a null hypothesis of equal rates
• H0 = total number of character changes / total duration of branches = average changes occurring along a branch per million years
• Randomly permute changes across the tree using this value (x 1,000) gives change per branch distribution
• Real values then compared to this distribution to search for significant excursions
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Method 2 - Randomisation branch test
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Method 3 - likelihood branch test
• Model no. of changes along branch i as a Poisson process with rate parameter i
• Test for equality of rates using likelihood ratio test:
H0: all i equal• Determine branches with significantly higher
or lower i
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Method 3 - likelihood branch test
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Method 4 - likelihood clade test
• Finally we were interested in applying a similar likelihood approach to ask the question of whether clades show a significant shift in tempo
• This approach is essentially the same as method 3, but instead of comparing one branch to the rest of the tree we compare the sum of all branches subtended by a node (i.e. a clade) with the rest of the tree
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Method 4 - likelihood clade test
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Conclusions
• We introduce four methods for examining the evolutionary tempo of discrete characters on a phylogeny
• These incorporate several corrections not used by previous workers
• Results allow simple interpretation of uncertainty in both dating and character optimisation, enabling greater confidence in any conclusions
• In sum, the results indicate a more nuanced pattern of lungfish evolution than suggested by previous workers