All models are wrong

Hickerson, Michael J.

doi:10.1111/mec.12794

Cited by 10 publications

(10 citation statements)

References 24 publications

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“…Approximate Bayesian computation (ABC; Beaumont, Zhang, & Balding, ) has been broadly applied in phylogeography (Bertorelle, Benazzo, & Mona, ; Hickerson, ), making it a suitable exemplar here. ABC was used to explore the circumstances under which a population with a history of lineage fusion carries signatures that are quantitatively different from long‐term panmixia within a single isolated population (Appendix S1).…”

Section: Approachmentioning

confidence: 99%

Extending phylogeography to account for lineage fusion

Garrick

Banusiewicz

Burgess

et al. 2019

Journal of Biogeography

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Secondary contact between long isolated populations has several possible outcomes. These include the strengthening of preexisting reproductive isolating mechanisms via reinforcement, the emergence of a hybrid lineage that is distinct from its extant parental lineages and which occupies a spatially restricted zone between them, or complete merging of two populations such that parental lineages are no longer extant ("lineage fusion" herein). The latter scenario has rarely been explicitly considered in single-species and comparative phylogeographic studies, yet it has the potential to impact inferences about population history and levels of congruence. In this paper, we explore the idea that insights into past lineage fusion may now be possible, owing to the advent of next-generation sequencing. Using simulated DNA sequence haplotype datasets (i.e., loci with alleles comprised of a set of linked nucleotide polymorphisms), we examined basic requirements (number of loci and individuals sampled) for identifying cases when a present-day panmictic population is the product of lineage fusion, using an exemplar statistical frameworkapproximate Bayesian computation. We found that with approximately 100 phased haplotype loci (each 400 bp long) and modest sample sizes of individuals (10 per population), lineage fusion can be detected under rather challenging scenarios. This included some scenarios where reticulation was fully contained within a Last Glacial Maximum timeframe, provided that mixing was symmetrical, ancestral gene pools were moderately to deeply diverged, and the lag time between the fusion event and gene pool sampling was relatively short. However, the more realistic case of asymmetrical mixing is not prohibitive if additional genetic data (e.g., 400 loci) are available.Notwithstanding some simplifying assumptions of our simulations and the knowledge gaps that remain about the circumstances under which lineage fusion is potentially detectable, we suggest that the recent release from data limitation allows phylogeographers to expand the scope of inferences about long-term population history.

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Section: Approachmentioning

confidence: 99%

Extending phylogeography to account for lineage fusion

Garrick

Banusiewicz

Burgess

et al. 2019

Journal of Biogeography

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“…It should, however, be straightforward to extend our approach for dealing with other more complex scenarios. Indeed, the flexibility of ABC allows the relative classification of quite specific models of evolution and demography, but also allows comparisons between previously tested models with new and more complex ones (Hickerson ). Of course, the results of any model comparison need to be interpreted with caution, given that they are ultimately informative only about the models actually considered and require extensive validation using pseudo‐observed data sets (Marin et al .…”

Section: Discussionmentioning

confidence: 99%

Inferring the mode of origin of polyploid species from next‐generation sequence data

Roux

Pannell

2015

Molecular Ecology

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Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next-generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa-pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole-genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels.

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“…Although this is not the same as traditional hypothesis testing in the sense that there is not a null hypothesis to reject or fail to reject, we demonstrate that model‐based approaches are useful for choosing among a priori hypotheses to make meaningful inferences. We recognize that there are shortcomings to this strategy, most important of which is that we may not have considered a model that could be better supported by the data (Hickerson ). We chose to evaluate a set of models designed to test specific hypotheses because it is more tractable than trying to compare all possible models and provides more useful insights than comparing several models that do not have a meaningful biological interpretation.…”

Section: Discussionmentioning

confidence: 99%

Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex

et al. 2015

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Fragmented species complexes provide an interesting system for investigating biogeographic history and the present distribution of genetic variation. Recent advances in sequencing technology and statistical phylogeography enable the collection and rigorous analysis of large multilocus data sets, but designing studies that produce meaningful phylogeographic inferences remains challenging. We implemented a Bayesian model comparison approach to investigate previous biogeographic hypotheses while simultaneously inferring the presence of genetic structure in a chorus frog species complex. The Illinois chorus frog (Pseudacris illinoensis), originally described as a subspecies of the broadly distributed Strecker's chorus frog (Pseudacris streckeri), occurs in small, disjunct regions associated with scarce sand prairie habitats that have been impacted by human development. We used high-throughput sequencing to develop and collect a multitiered genetic data set comprised of three different marker types (23 anonymous nuclear sequence loci, four mitochondrial genes and 14 microsatellite loci) designed to address questions across different evolutionary timescales. Phylogenetic analyses uncovered a deep divergence between populations in the Edwards Plateau of central Texas and all other P. streckeri/P. illinoensis populations, but suggest the disjunct distribution of P. illinoensis occurred more recently. Our best-supported migration model is consistent with the hypothesis that central Texas represented a refugium from which populations expanded via multiple routes. This model also indicates that disjunct northern and southern regions of P. illinoensis should be considered genetically distinct management units. Our study provides an evolutionary context for future studies and conservation efforts in P. illinoensis and demonstrates the utility of model-based approaches for phylogeographic inference.

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All models are wrong

Cited by 10 publications

References 24 publications

Extending phylogeography to account for lineage fusion

Extending phylogeography to account for lineage fusion

Inferring the mode of origin of polyploid species from next‐generation sequence data

Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex

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