publication . Article . 2018

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

Kühnert Denise; Stadler Tanja; Vaughan Timothy G.; Drummond Alexei J.;
Open Access
  • Published: 13 Nov 2018 Journal: Molecular Biology and Evolution, volume 33, pages 2,102-2,116 (issn: 0737-4038, eissn: 1537-1719, Copyright policy)
  • Publisher: Oxford University Press (OUP)
Abstract
When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth–death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic d...
Subjects
free text keywords: Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Outbreak, Virology, Phylogeography, Transmission (mechanics), law.invention, law, Evolutionary biology, Bayes' theorem, Population structure, Joint reconstruction, Viral phylodynamics, Population, education.field_of_study, education, Biology, Methods, Bayesian inference, infectious diseases, birth-death model, epidemiology, biogeography
Funded by
EC| PHYPD
Project
PHYPD
New phylogenetic methods for inferring complex population dynamics
  • Funder: European Commission (EC)
  • Project Code: 335529
  • Funding stream: FP7 | SP2 | ERC
40 references, page 1 of 3

Anderson CNK Ramakrishnan U Chan YL Hadly EA.2005 Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bi oinformatics 21(8): 1733–1734.15564305 [PubMed]

Balode D Ferdats A Dievberna I Viksna L Rozentale B Kolupajeva T Konicheva V Leitner T.2004 Rapid epidemic spread of HIV type 1 subtype A1 among intravenous drug users in Latvia and slower spread of subtype B among other risk groups. AIDS Res Hum Retroviruses. 20(2): 245–249.15018713 [OpenAIRE] [PubMed]

Bedford T Cobey S Beerli P Pascual M.2010 Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). PLoS Pathog. 6(5):e1000918.20523898 [OpenAIRE] [PubMed]

Beerli P Felsenstein J.1999 Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152(2): 763–773.10353916 [OpenAIRE] [PubMed]

Beerli P Felsenstein J.2001 Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci U S A. 98(8): 4563–4568.11287657 [OpenAIRE] [PubMed]

Beerli P Palczewski M.2010 Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics 185(1): 313–326.20176979 [OpenAIRE] [PubMed]

Bloomquist EW Lemey P Suchard MA.2010 Three roads diverged? Routes to phylogeographic inference. Trends Ecol Evol. 25(11): 626–632.20863591 [OpenAIRE] [PubMed]

Bouckaert R Heled J Kühnert D Vaughan T Wu CH Xie D Suchard MA Rambaut A Drummond AJ.2014 BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 10(4):e1003537.24722319 [OpenAIRE] [PubMed]

Davis MP Midford PE Maddison W.2013 Exploring power and parameter estimation of the BiSSE method for analyzing species diversification. BMC Evol Biol. 13:38.23398853 [OpenAIRE] [PubMed]

Drummond AJ Ho SYW Phillips MJ Rambaut A.2006 Relaxed phylogenetics and dating with confidence. PLoS Biol. 4(5):e88.16683862 [OpenAIRE] [PubMed]

Durrett R Levin S.1994 The importance of being discrete (and spatial). Theor Popul Biol. 46: 363–394.

Ewing G Nicholls G Rodrigo A.2004 Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations. Genetics 168(4): 2407–2420.15611198 [OpenAIRE] [PubMed]

Ewing G Rodrigo A 2006 Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden. Evol Bioinform Online.2:227–235. PMID: 19455215 PMCID: 2674663.19455215 [OpenAIRE] [PubMed]

Faria NR Suchard MA Rambaut A Streicker DG Lemey P.2013 Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints. Philos Trans R Soc Lond B Biol Sci. 368(1614): 20120196.23382420 [OpenAIRE] [PubMed]

FitzJohn RG Maddison WP Otto SP.2009 Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst Biol. 58(6): 595–611.20525612 [OpenAIRE] [PubMed]

40 references, page 1 of 3
Abstract
When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth–death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic d...
Subjects
free text keywords: Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Outbreak, Virology, Phylogeography, Transmission (mechanics), law.invention, law, Evolutionary biology, Bayes' theorem, Population structure, Joint reconstruction, Viral phylodynamics, Population, education.field_of_study, education, Biology, Methods, Bayesian inference, infectious diseases, birth-death model, epidemiology, biogeography
Funded by
EC| PHYPD
Project
PHYPD
New phylogenetic methods for inferring complex population dynamics
  • Funder: European Commission (EC)
  • Project Code: 335529
  • Funding stream: FP7 | SP2 | ERC
40 references, page 1 of 3

Anderson CNK Ramakrishnan U Chan YL Hadly EA.2005 Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bi oinformatics 21(8): 1733–1734.15564305 [PubMed]

Balode D Ferdats A Dievberna I Viksna L Rozentale B Kolupajeva T Konicheva V Leitner T.2004 Rapid epidemic spread of HIV type 1 subtype A1 among intravenous drug users in Latvia and slower spread of subtype B among other risk groups. AIDS Res Hum Retroviruses. 20(2): 245–249.15018713 [OpenAIRE] [PubMed]

Bedford T Cobey S Beerli P Pascual M.2010 Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). PLoS Pathog. 6(5):e1000918.20523898 [OpenAIRE] [PubMed]

Beerli P Felsenstein J.1999 Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152(2): 763–773.10353916 [OpenAIRE] [PubMed]

Beerli P Felsenstein J.2001 Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci U S A. 98(8): 4563–4568.11287657 [OpenAIRE] [PubMed]

Beerli P Palczewski M.2010 Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics 185(1): 313–326.20176979 [OpenAIRE] [PubMed]

Bloomquist EW Lemey P Suchard MA.2010 Three roads diverged? Routes to phylogeographic inference. Trends Ecol Evol. 25(11): 626–632.20863591 [OpenAIRE] [PubMed]

Bouckaert R Heled J Kühnert D Vaughan T Wu CH Xie D Suchard MA Rambaut A Drummond AJ.2014 BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 10(4):e1003537.24722319 [OpenAIRE] [PubMed]

Davis MP Midford PE Maddison W.2013 Exploring power and parameter estimation of the BiSSE method for analyzing species diversification. BMC Evol Biol. 13:38.23398853 [OpenAIRE] [PubMed]

Drummond AJ Ho SYW Phillips MJ Rambaut A.2006 Relaxed phylogenetics and dating with confidence. PLoS Biol. 4(5):e88.16683862 [OpenAIRE] [PubMed]

Durrett R Levin S.1994 The importance of being discrete (and spatial). Theor Popul Biol. 46: 363–394.

Ewing G Nicholls G Rodrigo A.2004 Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations. Genetics 168(4): 2407–2420.15611198 [OpenAIRE] [PubMed]

Ewing G Rodrigo A 2006 Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden. Evol Bioinform Online.2:227–235. PMID: 19455215 PMCID: 2674663.19455215 [OpenAIRE] [PubMed]

Faria NR Suchard MA Rambaut A Streicker DG Lemey P.2013 Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints. Philos Trans R Soc Lond B Biol Sci. 368(1614): 20120196.23382420 [OpenAIRE] [PubMed]

FitzJohn RG Maddison WP Otto SP.2009 Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst Biol. 58(6): 595–611.20525612 [OpenAIRE] [PubMed]

40 references, page 1 of 3
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publication . Article . 2018

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

Kühnert Denise; Stadler Tanja; Vaughan Timothy G.; Drummond Alexei J.;