# Inference of population history using coalescent HMMs: review and outlook.

@article{Spence2018InferenceOP, title={Inference of population history using coalescent HMMs: review and outlook.}, author={Jeffrey P. Spence and Matthias Steinr{\"u}cken and Jonathan Terhorst and Yun S. Song}, journal={Current opinion in genetics \& development}, year={2018}, volume={53}, pages={ 70-76 } }

Studying how diverse human populations are related is of historical and anthropological interest, in addition to providing a realistic null model for testing for signatures of natural selection or disease associations. Furthermore, understanding the demographic histories of other species is playing an increasingly important role in conservation genetics. A number of statistical methods have been developed to infer population demographic histories using whole-genome sequence data, with recent…

## 32 Citations

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The method CHIMP (CHMM History-Inference ML Procedure), a novel CHMM method for inferring the size history of a population, is presented and is agnostic to the phasing of the data, which makes it a promising alternative in scenarios where high quality data is not available and has potential applications for pseudo-haploid data.

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A tool inferring the best case convergence of SMC methods assuming the true underlying coalescent genealogies are known, and a new interpretation ofSMC methods by highlighting the importance of the transition matrix, which is argued can be used as a set of summary statistics in other statistical inference methods.

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- Medicine, GeographyProceedings of the National Academy of Sciences
- 2019

DiCal2, an efficient, flexible statistical method that can use whole-genome sequence data from multiple populations to infer complex demographic models involving population size changes, population splits, admixture, and migration, is presented.

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- Biology, Computer Science
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The limits of this methodology are explored and a tool is presented that can be used to help users quantify what information can be confidently retrieved from given datasets to study the consequences for inference accuracy violating the hypotheses and the assumptions of SMC approaches.

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- Medicine, BiologyGenetics
- 2019

An algorithm for inferring ancestry segments and characterizing admixture events, which involve an arbitrary number of genetically differentiated groups coming together, which allows inference of the demographic history of the species, properties of admixing groups, identification of signatures of natural selection, and may aid disease gene mapping.

Demographic inference

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- 2021

The next generation sequencing revolution has multiplied the amount of genetic data for many organisms by orders of magnitude, and new genomic data can be used to infer the past demographic history of populations.

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- Biology, Computer Science
- 2020

This work derives fast, exact methods for frequentist and Bayesian inference using SMC, which requires minimal user intervention or parameter tuning, no numerical optimization or E-M, and is faster and more accurate.

EXACT DECODING OF THE SEQUENTIALLY MARKOV COALESCENT

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In statistical genetics, the sequentially Markov coalescent (SMC) is an important framework for approximating the distribution of genetic variation data under complex evolutionary models. Methods…

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- 2019

It was found that the details of sampling intervals that pass a four‐gamete filter have a moderate effect, and that schemes that use the longest intervals, or that use overlapping intervals, gave poorer results, suggesting that filtering based on the four-gamete criterion, while necessary for methods like these, leads to reduced resolution on migration.

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