Specimens, with a specially designed stacking sequence, which allows migration events using a simple Double Cantilever Beam set-up, were tested for θ = 75° and 60°.
The exact events used to represent a VM stopping or starting as a result of migration may differ depending on the underlying hypervisor.
Comparisons between the tree height and migration event counts obtained using our sampler (2 × 10 steps minus 2 × 10 burn-in) and those obtained through 10 direct simulations generated using MASTER (Vaughan and Drummond, 2013) for trees with five leaves having times 0, 5, 10, 15, 20 and locations 0, 1, 2, 3, 0 in a 4 deme model with θ d = 7 and m dd ′ = 0.05 for all d, d ′ are shown in Figure 3.
Evidence of recent migration events across clusters was assessed using the Bayesian multilocus genotyping procedure implemented with MCMC methods in BayesAss v.1.3 [ 22].
Migration events throughout the phylogeny were reconstructed using a reversible discrete phylogeographic model46 with a CTMC rate reference prior47.
The analytical dataset used data on migration events and socio-demographic characteristics which were collected prior to the HIV test date.
We did not use TreeMix to infer migration events because this software models migration between populations as occurring at a single instantaneous time point35, an assumption that is quite unrealistic for domestic species.
A section of the original hemagglutinin maximum likelihood tree was used to map the migration events for 67 samples of a single clade 2.3 H5N1 strain circulating in southern China 2005 2006 (Table S1, Figure 2a,b).
Growth rates of mitochondrial haplogroups were estimated with Lamarc v2.2 [48] using a bayesian framework allowing migrations across haplogroups (with a maximum of 10000 migration events, default priors used for migration rates estimation).
Here, maximum-likelihood trees of Chinese pig populations without migration events and with 6 migration events were tested by using the Chinese wild boars as the outgroup population.
