<scp>IM</scp>a2p – parallel <scp>MCMC</scp> and inference of ancient demography under the Isolation with migration (<scp>IM</scp>) model

Sethuraman, Arun; Hey, Jody

doi:10.1111/1755-0998.12437

Cited by 71 publications

(68 citation statements)

References 15 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

Self Cite

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“…Our extensive sequence data are more likely to meet the mutation models assumed in many coalescent-based demographic inference programs that test models of isolation with migration (IMA2p software, Hey, 2010a;Hey, 2010b;Sethuraman & Hey, 2016). Our extensive sequence data are more likely to meet the mutation models assumed in many coalescent-based demographic inference programs that test models of isolation with migration (IMA2p software, Hey, 2010a;Hey, 2010b;Sethuraman & Hey, 2016).…”

Section: Introductionmentioning

confidence: 98%

Amplicon sequencing of 42 nuclear loci supports directional gene flow between South Pacific populations of a hydrothermal vent limpet

Plouviez

LaBella

Weisrock

et al. 2019

Ecology and Evolution

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In the past few decades, population genetics and phylogeographic studies have improved our knowledge of connectivity and population demography in marine environments. Studies of deep‐sea hydrothermal vent populations have identified barriers to gene flow, hybrid zones, and demographic events, such as historical population expansions and contractions. These deep‐sea studies, however, used few loci, which limit the amount of information they provided for coalescent analysis and thus our ability to confidently test complex population dynamics scenarios. In this study, we investigated population structure, demographic history, and gene flow directionality among four Western Pacific hydrothermal vent populations of the vent limpet Lepetodrilus aff. schrolli. These vent sites are located in the Manus and Lau back‐arc basins, currently of great interest for deep‐sea mineral extraction. A total of 42 loci were sequenced from each individual using high‐throughput amplicon sequencing. Amplicon sequences were analyzed using both genetic variant clustering methods and evolutionary coalescent approaches. Like most previously investigated vent species in the South Pacific, L. aff. schrolli showed no genetic structure within basins but significant differentiation between basins. We inferred significant directional gene flow from Manus Basin to Lau Basin, with low to no gene flow in the opposite direction. This study is one of the very few marine population studies using >10 loci for coalescent analysis and serves as a guide for future marine population studies.

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“…To test these predictions, we estimated the rate and direction of gene flow between regions in a pairwise manner (e.g. CT vs. IO and CT vs. PO) using the coalescent Isolation with Migration (IMa) model (Hey & Nielsen, ; Nielsen & Wakeley, ) as implemented in IMa2 and IMa2p packages (Sethuraman & Hey, ). A pairwise approach rather than a full model was implemented to circumvent the problem of giving an a priori historical scenario (e.g.…”

Section: Methodsmentioning

confidence: 99%

Revisiting the “Centre Hypotheses” of the Indo‐West Pacific: Idiosyncratic genetic diversity of nine reef species offers weak support for the Coral Triangle as a centre of genetic biodiversity

Matias

Riginos

2018

Journal of Biogeography

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Aim Several biogeographic hypotheses seek to explain the extreme species diversity of the coral reefs in the Coral Triangle (CT) of the Indo‐West Pacific (IWP). Here, we investigate processes implicit to the Centre of Origin, Centre of Overlap and Centre of Survival hypotheses. We focus on intraspecific genetic data, where intraspecific diversity can provide information regarding directionality of past dispersal (gene flow) and changes in population size such as expansion from refugia. Location Indian Ocean, Coral Triangle and West Pacific Ocean. Methods We use existing mitochondrial DNA data augmented with new samples from the Philippines, thus filling in key sampling gaps from previous studies, to examine nine reef species. We first test if genetic diversity peaks in the CT. We then estimate gene flow between regions—CT vs. Indian Ocean (IO) and CT vs. Pacific Ocean (PO)—to assess concordance with predicted directions of movement (i.e. into the CT or out of the CT). Finally, we investigate the historical demography of these species and evaluate population expansions to ascertain whether genetic diversity is correlated with putative Pleistocene refugia. Results Genetic diversity in the CT was not greater than genetic diversity in the IO and PO, and we found highly variable spatial patterns of genetic diversity when species were evaluated individually. Gene flow estimates indicated very limited exchange between regions, consistent with peripheral isolation and/or signals of historical divergence. For some species, however, there were signals of movement out of the CT. While there was no significant correlation between genetic diversity and putative refugia, genetic patterns suggested that some populations have experienced population expansions. The locations of expansion were also variable across species. Overall, there was no signal of concordant processes shaping intraspecific genetic diversity. Main conclusions Genetic patterns across species were highly variable with some species lending weak support for processes aligned with each of the “Centre” of diversity hypotheses. But overall there was no compelling evidence for uniform processes underlying all species, which possibly indicate that processes underlying the different “Centre” have not strongly affected IWP species within the recent past.

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IMa2p – parallel MCMC and inference of ancient demography under the Isolation with migration (IM) model

Cited by 71 publications

References 15 publications

Recent advances in conservation and population genomics data analysis

Recent advances in conservation and population genomics data analysis

Amplicon sequencing of 42 nuclear loci supports directional gene flow between South Pacific populations of a hydrothermal vent limpet

Revisiting the “Centre Hypotheses” of the Indo‐West Pacific: Idiosyncratic genetic diversity of nine reef species offers weak support for the Coral Triangle as a centre of genetic biodiversity

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