In the Light of Evolution Volume X: Comparative Phylogeography (2017) / Chapter Skim
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7 Phylogeographic Model Selection Leads to Insight into the Evolutionary History of Four-Eyed Frogs - Maria Tereza C. Thom and Bryan C. Carstens
7 Phylogeographic Model Selection Leads to Insight into the Evolutionary History of Four-Eyed Frogs - Maria Tereza C. Thom and Bryan C. Carstens
Pages 137-154
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From page 137... ...
However, the actual inferences made by phylogeog raphers remain dependent on qualitative interpretations derived from these parameters' values and as such may be subject to overinterpreta tion and confirmation bias. Here we argue in favor of using an objective approach to phylogeographic inference that proceeds by calculating the probability of multiple demographic models given the data and the sub sequent ranking of these models using information theory.
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From page 138... ...
Despite the potential complexr ity of the demographic models, the actual process of phylogeographic inference remains largely analogous to that of earlier investigations: The relative influence of evolutionary processes is derived from the magnitude of numeric values estimated for parameters that measure what the r esearchers believe to be important evolutionary processes. For example, subjective decisions regarding estimated rates of gene flow are commonly
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From page 139... ...
, whereas those working on focal taxa that inhabit island systems are likely to consider dispersal to be a key process shaping allele frequencies, and estimate effective population sizes under migration models (e.g., Beerli and Felsenstein, 2001)
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From page 140... ...
In fact, the real complexity of the demography of natural populations is unlikely to be captured by any simple model we could propose. In some cases, this may not affect inferences much, but in other cases it will." If phylogeographic inferences are largely derived from parameter estimates made under complex models, then such inferences are implicitly conditioned on the statistical fit of the model used to estimate these parameters to the empirical data collected from the focal system.
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From page 141... ...
If the goal of phylogeography is to infer the evolutionary history of the focal taxon, then ranking a set of models that represent alternative evolutionary scenarios provides a rigorous tool for inference because it will help researchers to avoid confirmation bias. Because the parameters in each model correspond to various evolutionary processes, the relative influence of particular evolutionary processes to the empirical system can be assessed by considering the set of parameters included in the model that offers the best fit to the data.
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From page 142... ...
CASE STUDY: THE PLEURODEMA SYSTEM IN THE BRAZILIAN CAATINGA Pleurodema alium and Pleurodema diplolister are sister species of foureyed frogs that inhabit the Caatinga in northeastern Brazil (Faivovich et al., 2012)
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From page 143... ...
Although range size and effective population size are not necessarily correlated, the difference in geographic range provides justification for allowing for the possibility of differences in effective population size among species, so long as we assume that the mutation rate does not vary between species. In addition to the processes of temporal divergence and different population sizes, other evolutionary processes could be important: population size change within species (such as population bottlenecks or exponential population growth)
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From page 144... ...
. DNA digestion and barcode ligation were performed individually for each sample using 300 ng of freshly extracted DNA, the restriction enzymes Sbf1-HF and MspI, the ligation enzyme Ligase T4, and eight different barcoded Illumina adaptors.
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From page 145... ...
. Except for the initial demultiplexing step, which was conducted separately on each library, we processed data for all samples together with the following parameter specifications: 10× minimal coverage, four or fewer unknown bases per sequence, minimum
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From page 146... ...
Alternatively, removing all loci that contain missing data will dramatically reduce the size of any observed RADseq dataset and negate some of the advantages of collecting such data in the first place. Because we analyze our data using a method that relies on estimates of the population site frequency spectra (discussed below)
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From page 147... ...
After the demographic model is specified, FSC2 selects initial parameter values at random from a range specified by the user and simulates data using the demographic model and parameter values. Composite likelihoods are calculated following Nielsen (2000)
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This example illustrates the importance of performing phylogeographic model selection before any attempt to make inferences about the evolutionary history of a system, especially those based on parameter estimates.
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From page 149... ...
, the time that expansion begins (Tevent) , and the magnitude of population size change (Gexp)
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From page 150... ...
Carstens Phylogeographic Inferences There are several advantages to basing phylogeographic inferences on the results of model selection exercises. Such analyses allow researchers to identify which evolutionary processes have shaped genetic diversity.
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From page 151... ...
New Data, Better Methods, and Improved Inferences from Nonmodel Organisms One of the pressing issues facing the discipline of phylogeography in the past was the limited amount of genetic data that could be collected from most systems, and the poor quality of parameter estimates that
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From page 152... ...
diplolister. Shown clockwise from upper left are estimates of the current ecological niche, as well as projections of this niche onto past conditions of the mid-Holocene, the LGM, and the LIG.
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From page 153... ...
, which implements a divergence with gene flow model, can be used to conduct model selection using either likelihood ratio tests (e.g., Hey and Nielsen, 2007) or information theoretic approaches (Carstens et al., 2009)
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From page 154... ...
It is incumbent on researchers who do not conduct model selection as part of their phylogeographic investigations to ask whether their phylogeographic inferences are based on a model of historical demography that is appropriate for their empirical system. ACKNOWLEDGMENTS We thank Célio F
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