Isolation with Migration Models for More Than Two Populations

Hey, Jody

doi:10.1093/molbev/msp296

Cited by 799 publications

(862 citation statements)

References 40 publications

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“…A prominent set of tools for this analysis includes IM, IMa, IMa2, and IMa2p (Hey, 2010; Hey, Chung, & Sethuraman, 2015; Hey & Nielsen, 2007; Sethuraman & Hey, 2015). In general, these methods utilize a Bayesian Metropolis‐coupled Markov Chain Monte Carlo (MCMCMC) method to estimate effective population sizes, migration rates, and divergence times under the IM model from haplotypic data.…”

Section: Improving Downstream Computational Analysesmentioning

confidence: 99%

Recent advances in conservation and population genomics data analysis

Hendricks

Anderson

Antão

et al. 2018

Evolutionary Applications

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New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.

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Section: Improving Downstream Computational Analysesmentioning

confidence: 99%

Recent advances in conservation and population genomics data analysis

Hendricks

Anderson

Antão

et al. 2018

Evolutionary Applications

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show abstract

“…The program IMa2 (Hey, 2010) was used to infer divergence time and the level of gene flow between A. compressiceps and A. calvus based on an isolationwith-migration (IM) coalescent model (Hey & Nielsen, 2004. Isolation-with-migration models and pure isolation models were each fit to datasets including lake-wide samples or a subset of samples from the area of sympatry.…”

Section: Species Divergence and Demographic Historymentioning

confidence: 99%

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

et al. 2016

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Stenotopic specialization to a fragmented habitat promotes the evolution of genetic structure. It is not yet clear whether small-scale population structure generally translates into large-scale intraspecific divergence. In the present survey of mitochondrial genetic structure in the Lake Tanganyika endemic Altolamprologus (Teleostei, Cichlidae), a rock-dwelling cichlid genus comprising A. compressiceps and A. calvus, habitat-induced population fragmentation contrasts with weak phylogeographic structure and recent divergence among genetic clades. Low rates of dispersal, perhaps along gastropod shell beds that connect patches of rocky habitat, and periodic secondary contact during lake level fluctuations are apparently sufficient to maintain genetic connectivity within each of the two Altolamprologus species. The picture of genetic cohesion was interrupted by a single highly divergent haplotype clade in A. compressiceps restricted to the northern part of the lake. Comparisons between mitochondrial and nuclear phylogenetic reconstructions suggested that the divergent mitochondrial clade originated from ancient interspecific introgression. Finally, 'isolation-with-migration' models indicated that divergence between the two Altolamprologus species was recent (67-142 KYA) and proceeded with little if any gene flow. As in other rock-dwelling cichlids, recent population expansions were inferred in both Altolamprologus species, which may be connected with drastic lake level fluctuations.

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“…Potential gene flow among major lineages or species was estimated using the isolation with migration (IM) model with the program IMA2 (version 8.27.2012;Hey, 2010;Hey and Nielsen, 2007). The method estimates the density functions and posterior-probability densities of the IM model parameters using a Markov chain (MCMC) method (Hey and Nielsen, 2007).…”

Section: Gene Flow Estimationmentioning

confidence: 99%

“…It is widely acknowledged that speciation with ongoing gene flow is common (Nadachowska and Babik, 2009;Nosil, 2008). The detected levels of gene flow (2Nm = 0.28-0.35) represent substantial gene flow but not high enough to prevent divergence; a 2Nm greater than one would limit the divergence process in the absence of selection (Hey, 2010). The phylogenetic relationships within the A. mantzorum group remain largely unresolved.…”

Section: Species Diversity In the Amolops Mantzorum Groupmentioning

confidence: 99%

A phylogeographic evaluation of the Amolops mantzorum species group: Cryptic species and plateau uplift

2014

Molecular Phylogenetics and Evolution

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Isolation with Migration Models for More Than Two Populations

Cited by 799 publications

References 40 publications

Recent advances in conservation and population genomics data analysis

Recent advances in conservation and population genomics data analysis

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

A phylogeographic evaluation of the Amolops mantzorum species group: Cryptic species and plateau uplift

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