Description of the phylogeographic models with an emphasis on data source and quality.
Supplementary Table 2 is also available in Excel format here.
| Phylodynamics category | Model description | Software | Genetic sequences | Sequence length (pb) | Data source | Parameters inferred | Reference |
|---|---|---|---|---|---|---|---|
| Parsimony discrete phylogeography | Maximum parsimony | PAUP* | N (n = 130) | 1335 | Not informed | Nucleotide substitution rate, Migration rates, tMRCA | Bourhy et al., 2008 |
| Bayesian discrete phylogeography | Symmetric DTA + BSSVS | BEAST 1 | N (n = 101) | 1335 | Bourhy et al., 2008 | Migration rates | Lemey et al., 2009 |
| Parsimony discrete phylogeography | Maximum parsimony | PAUP* |
N (n = 231) G (n = 34) |
1335 1572 |
Passive | Nucleotide substitution rate, Migration rates, tMRCA | Talbi et al., 2009 |
| Parsimony discrete phylogeography |
DELTRAN and ACCTRAN optimization Monte Carlo simulations |
MigraPhyla | N (n = 200) | 1353 |
Passive GenBank |
Nucleotide substitution rate, Migration rates, tMRCA | Meng et al., 2011 |
| Bayesian discrete phylogeography | DTA + BSSVSa | BEAST 1 | N (n = 303) | 405 |
Passive GenBank |
Migration rates, Root state, tMRCA | Hayman et al., 2011 |
| Bayesian discrete phylogeography | Symmetric DTA + BSSVS | BEAST 1 | N (n = 71) | 1332 | GenBank | Nucleotide substitution rate, Migration rates, tMRCA | Carnieli et al., 2011 |
| Parsimony discrete phylogeography |
DELTRAN optimization Monte Carlo simulations |
PAUP* MigraPhyla |
N (n = 210) | 720 |
Active Passive |
Nucleotide substitution rate, Migration rates, tMRCA | Yu et al., 2012 |
| Bayesian discrete phylogeography | Asymmetric DTA + BSSVS | BEAST 1 | intergenic G-L (n = 635) | 590 | GenBank | Migration rates, Root state, tMRCA | Mollentze et al., 2013 |
| Bayesian discrete phylogeography | Symmetric DTA + BSSVS | BEAST 1 | N (n = 232) | 1353 |
Active Passive |
Nucleotide substitution rate, Migration rates, tMRCA | Guo et al., 2013 |
| Bayesian continuous phylogeography | Relaxed random walk (lognormal prior) | BEAST 1 | N (n = 53) | 1388 |
Passive GenBank |
Nucleotide substitution rate, Lineage velocity, tMRCA | Carnieli et al., 2013 |
| Bayesian discrete phylogeography | Symmetric DTA + BSSVS | BEAST 1 | G (n = 263) | 1572 | Passive | Nucleotide substitution rate, Markov jumps, Migration rates, tMRCA | Tohma et al., 2014 |
| Bayesian discrete phylogeography | Symmetric DTA + BSSVS | BEAST 1 | N (n = 139) | 400 |
Passive Systematic |
Markov jumps, Migration rates, Root state, tMRCA | Horton et al., 2015 |
| Bayesian discrete phylogeography | Asymmetric DTA + BSSVS | BEAST 1 |
partial N gene (n = 430) N (n = 100) whole genome (n = 58) |
405 1350 - |
Active Passive |
Nucleotide substitution rate, Markov jumps, Migration rates, Population dynamics | Brunker et al., 2015 |
| Bayesian discrete phylogeography | Symmetric DTA + BSSVS | BEAST 1 | N (n = 62) | 534 | Passive | Migration rates, Root state | Dibia et al., 2015 |
| Bayesian discrete phylogeography | Symmetric DTA + BSSVS | BEAST 1 | N (n = 203) | 1353 | GenBank | Migration rates | Yao et al., 2015 |
| Bayesian phylodynamics | Coalescent models | BEAST 1 | Whole genome (n = 248) |
GenBank WHO Collaborative Center for Reference and Research on Rabies French National Reference Centre for Rabies |
Nucleotide substitution rate, tMRCA | Troupin et al., 2016 | |
| Bayesian discrete phylogeography | Asymmetric DTA + BSSVS | BEAST 1 | N (n = 401) | 1350 |
Active Passive |
Nucleotide substitution rate, Markov jumps, Migration rates | Zhang et al., 2017 |
| Bayesian discrete phylogeography | Asymmetric DTA + BSSVS | BEAST 1 |
N (n = 20) G (n = 16) |
1353 1575 |
Passive | Nucleotide substitution rate, Migration rates, tMRCA | Ma et al., 2017 |
| Bayesian continuous phylogeography | Relaxed random walk (lognormal prior) | BEAST 1 | N, P, intergenic G-L (n = 250) | 3080 | Talbi et al., 2009 |
Velocity, distance and duration of movement Velocity-associated landscape features |
Dellicour et al., 2017 |
|
Bayesian discrete phylogeography Bayesian continuous phylogeography |
Asymmetric GLM + BSSVS Relaxed random walk (gamma prior) |
BEAST 1 | Whole genome (n = 152) |
Brunker et al., 2015 Not indicated |
Nucleotide substitution rate, Markov jumps, Migration rates Velocity, distance and duration of movement Velocity-associated landscape features |
Brunker et al., 2018 | |
| Bayesian discrete phylogeography | Symmetric DTA + BSSVS | BEAST 1 | N (n = 112) | 1353 | GenBank | Nucleotide substitution rate, Migration rates, Population dynamics, tMRCA | Wang et al., 2019 |
|
Bayesian discrete phylogeography Bayesian continuous phylogeography |
Symmetric DTA + BSSVS Relaxed random walk (not indicated) |
BEAST 1 | Whole genome (n = 101) | Passive |
Nucleotide substitution rate Direction of spread Velocity, distance and duration of movement Velocity- and direction-associated landscape features |
Dellicour et al., 2019 | |
| Note: | |||||||
| Abbreviations: ACCTRAN, Accelerated Transformation; BSSVS, Bayesian Stochastic Search Variable Selection; DELTRAN, Delayed Transformation; DTA, Discrete Trait Analysis; GLM, Generalized Linear Model; tMRCA, time to the Most Recent Common Ancestor; WHO World Health Organization | |||||||
| a Symmetry not indicated in the original publication |