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Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns

Laxmi Parida, Marta Melé, Francesc Calafell, Jaume Bertranpetit
2008 Journal of Computational Biology  
Driven by the need for a more complete analysis, we address the problem of estimating the ancestral recombination graph (ARG) from a collection of extant sequences.  ...  We exploit the coherence that is observed in the human haplotypes as patterns and present a network model of patterns to reconstruct the ARG.  ...  We are also thankful to Ajay Royyuru for his insightful comments on the work and bringing our attention to the tool Graphviz [GKNV93] : most of the networks in this paper are drawn using this software  ... 
doi:10.1089/cmb.2008.0065 pmid:18844583 fatcat:ppli7oqg2bfzzcphfhkvnjlm5q

ARG-walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis

Hao Chen, Peng Yang, Jing Guo, Chee Keong Kwoh, Teresa M Przytycka, Jie Zheng
2015 BMC Genomics  
Results In this work, we propose a novel graph mining algorithm named ARG-walker, based on random walks on ancestral recombination graphs (ARG), to estimate individualspecific recombination hotspot strengths  ...  These sub-networks are merged to construct the ARG represented as a directed graph G(V, E). Readers interested in details of the algorithm behind IRiS are referred to [20] [21] .  ...  Additional files Additional file 1 -Python and Perl scripts for generating simulation data Python scripts for generating simulated SNP data, and Perl scripts for pre-processing the SNP data as input  ... 
doi:10.1186/1471-2164-16-s12-s1 pmid:26679564 pmcid:PMC4682399 fatcat:2nv7dbmspvbftoeaw3kj3tmnly

Current Methods for Recombination Detection in Bacteria

Anton E. Shikov, Yury V. Malovichko, Anton A. Nizhnikov, Kirill S. Antonets
2022 International Journal of Molecular Sciences  
To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed  ...  , thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science.  ...  ancestral recombination graphs (ARGs) [63] .  ... 
doi:10.3390/ijms23116257 pmid:35682936 pmcid:PMC9181119 fatcat:qrp4jjmrxbavtdctlqhxoyqi74

SIA: Selection Inference Using the Ancestral Recombination Graph [article]

Hussein A Hejase, Ziyi Mo, Leonardo Campagna, Adam Siepel
2021 bioRxiv   pre-print
Inference using the Ancestral recombination graph (SIA).  ...  Coupling the rich information in the ancestral recombination graph (ARG) with a powerful and scalable deep learning framework, we developed a novel method to detect and quantify positive selection: Selection  ...  Acknowledgments The authors would like to acknowledge Noah Dukler for help with Figure 1  ... 
doi:10.1101/2021.06.22.449427 fatcat:2c7g4hkkjnas5ae4yjrs76nzzy

Evolutionary Phylogenetic Networks: Models and Issues [chapter]

Luay Nakhleh
2010 Problem Solving Handbook in Computational Biology and Bioinformatics  
Phylogenetic networks are special graphs that generalize phylogenetic trees to allow for modeling of non-treelike evolutionary histories.  ...  Several excellent surveys of the different flavors of phylogenetic networks and methods for their reconstruction have been written recently.  ...  The contents are solely the responsibility of the authors and do not necessarily represent the official views of the DOE, NSF, National Library of Medicine or the National Institutes of Health.  ... 
doi:10.1007/978-0-387-09760-2_7 fatcat:a7ugipi3fvdypgllt556bdkcqq

Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster ofAspergillus parasiticus

IGNAZIO CARBONE, JUDY L. JAKOBEK, JORGE H. RAMIREZ-PRADO, BRUCE W. HORN
2007 Molecular Ecology  
Phylogenetic network analyses showed a history of recombination between chemotype-specific haplotypes, as well as evidence of contemporary recombination.  ...  Estimates of Ka/Ks for representative cluster genes provide evidence of selection for OMST and AF chemotypes, and indicate a possible role of chemotypes in ecological adaptation and speciation.  ...  Coalescent simulations were performed, in part, on HPC resources provided by the NC State Information Technology Division with support from the Office of the Provost and Office of Research and Graduate  ... 
doi:10.1111/j.1365-294x.2007.03464.x pmid:17725568 fatcat:7ulbd32yerhc7mr72icc5sng4u

EFFICIENT COMPUTATION OF MINIMUM RECOMBINATION WITH GENOTYPES (NOT HAPLOTYPES)

Yufeng Wu, Dan Gusfield
2006 Computational Systems Bioinformatics  
We apply these algorithms to the goal of finding recombination hotspots, obtaining as good results as a published method that first infers haplotypes; and to the case of estimating the minimum amount of  ...  We present algorithms to solve downstream questions concerning the minimum amount of recombination needed to derive given genotypic data, without first fixing a choice of haplotypes.  ...  The authors wish to thank Yun S. Song for sharing simulation scripts. Work supported by grants CCF-0515278 and IIS-0513910 from National Science Foundation.  ... 
doi:10.1142/9781860947575_0021 fatcat:cfgkydybordjxjvjbyuyripjfm

EFFICIENT COMPUTATION OF MINIMUM RECOMBINATION WITH GENOTYPES (NOT HAPLOTYPES)

Yufeng Wu, Dan Gusfield
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
We apply these algorithms to the goal of finding recombination hotspots, obtaining as good results as a published method that first infers haplotypes; and to the case of estimating the minimum amount of  ...  We present algorithms to solve downstream questions concerning the minimum amount of recombination needed to derive given genotypic data, without first fixing a choice of haplotypes.  ...  The authors wish to thank Yun S. Song for sharing simulation scripts. Work supported by grants CCF-0515278 and IIS-0513910 from National Science Foundation.  ... 
doi:10.1142/1860947573_0024 fatcat:5orh3lsktzbzba3cjeu5ochpuy

EFFICIENT COMPUTATION OF MINIMUM RECOMBINATION WITH GENOTYPES (NOT HAPLOTYPES)

Yufeng Wu, Dan Gusfield
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
We apply these algorithms to the goal of finding recombination hotspots, obtaining as good results as a published method that first infers haplotypes; and to the case of estimating the minimum amount of  ...  We present algorithms to solve downstream questions concerning the minimum amount of recombination needed to derive given genotypic data, without first fixing a choice of haplotypes.  ...  The authors wish to thank Yun S. Song for sharing simulation scripts. Work supported by grants CCF-0515278 and IIS-0513910 from National Science Foundation.  ... 
doi:10.1142/18609475730024 fatcat:76nnht2lsbavtotexl2xexbjja

Genome-wide inference of ancestral recombination graphs [article]

Matthew D. Rasmussen, Melissa J. Hubisz, Ilan Gronau, Adam Siepel
2013 arXiv   pre-print
The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events  ...  However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in  ...  Figure Legends Figure Legends Fig. 1 : 1 An ancestral recombination graph (ARG) for four sequences.  ... 
arXiv:1306.5110v3 fatcat:4u3ru23f5vfk7k43d256vvzsne

Using ancestral information to detect and localize quantitative trait loci in genome-wide association studies

Katherine L Thompson, Laura S Kubatko
2013 BMC Bioinformatics  
Results: We evaluate the performance of the new method using simulated data, and find that it performs at least as well as existing methods with an increase in performance in the case of population structure  ...  Application of the methodology to a real data set consisting of high-density lipoprotein cholesterol measurements in mice shows the method performs well for empirical data, as well.  ...  Acknowledgements The authors would like to thank the two anonymous reviewers for their helpful comments on an earlier version of the manuscript.  ... 
doi:10.1186/1471-2105-14-200 pmid:23786262 pmcid:PMC3706278 fatcat:nzgk3pcye5ffvi5g2lgzasdqyy

Haplotyping Methods for Pedigrees

Guimin Gao, David B. Allison, Ina Hoeschele
2009 Human Heredity  
With the dramatic increase in the number of available single nucleotide polymorphism (SNP) markers, haplotype inference (haplotyping) using observed genotype data has become an important component of genetic  ...  As several authors noted, family and pedigree datasets are abundant and have unique advantages. In the past twenty years, many haplotyping methods for family and pedigree data have been developed.  ...  This research was supported by grant GM073766 from the National Institute of General Medical Sciences and supported in part by grants ES09912, CA100949, and P30DK056336 from the National Insti-tutes of  ... 
doi:10.1159/000194978 pmid:19172084 pmcid:PMC2692835 fatcat:fl6zfs7ehfbs7pssi4jyypfyoy

The Effect of Single Recombination Events on Coalescent Tree Height and Shape

Luca Ferretti, Filippo Disanto, Thomas Wiehe, Nadia Singh
2013 PLoS ONE  
Considering recombination as a process which acts along genomes and which creates sequence segments with shared ancestry, we study the influence of single recombination events upon tree characteristics  ...  The coalescent with recombination is a fundamental model to describe the genealogical history of DNA sequence samples from recombining organisms.  ...  Author Contributions Analyzed the data: LF TW. Wrote the paper: LF TW. Designed the study: TW LF. Performed calculations and derived theorems: LF FD. Performed computer simulations: LF TW.  ... 
doi:10.1371/journal.pone.0060123 pmid:23593168 pmcid:PMC3620475 fatcat:gbsardgjrjfzrbylqd25bt3rra

Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization [article]

R.A.L. Elworth, H.A. Ogilvie, J. Zhu, L. Nakhleh
2018 arXiv   pre-print
They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters, such as divergence times and population sizes, they form a generative process of molecular  ...  In particular, parsimony, likelihood, and Bayesian methods have been devised for estimating phylogenetic networks and associated parameters using estimated gene trees as data.  ...  This focus led to work on inference of smallest phylogenetic networks that display a given set of trees, as well as on comparing networks in terms of their displayed trees.  ... 
arXiv:1808.08662v1 fatcat:par4fybfkrdu5m4bfiunqgs4xm

Old divergence and restricted gene flow between torrent duck (Merganetta armata ) subspecies in the Central and Southern Andes

Luis Alza, Philip Lavretsky, Jeffrey L. Peters, Gerardo Cerón, Matthew Smith, Cecilia Kopuchian, Andrea Astie, Kevin G. McCracken
2019 Ecology and Evolution  
To investigate the structure and rate of gene flow among populations of habitat-specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical  ...  Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru, n = 10 and Argentina, n = 9) was subjected to partial  ...  Priors were defined as follows: Θ PERU = 80, Θ ARGENTINA = 60, Θ ANCESTRAL = 150, m PER.-ARG. = 10, m ARG.  ... 
doi:10.1002/ece3.5538 pmid:31534707 pmcid:PMC6745679 fatcat:42nc4kxaybbtzdngzrdv4d65ly
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