The population assignment test correctly assigned 80.59% of the individuals to their original population.
Because genetic divergence decreases due to gene flow after secondary contact, we restricted this analysis to our genetically pure parental populations, by combining all the "pure" individuals assigned to the same population (assignment pp≥0.95) and calculating Nei's D [ 59] with GENETIX [ 60].
The model with three populations performed poorly in assigning samples of the Water Rail to two clusters, the highest population assignment probability for membership of an individual to clusters 2 and 3 being only 0.571 (0, 1.0).
We used the population assignment tests implemented in BAPS and STRUCTURE and two algorithmic species delimitation procedures (ABGD, GMYC) to generate species boundary discovery hypotheses, which were subsequently tested using Bayes factors.
However, the percentage of isolates with trichothecene genotypes that were not predictive of their genetic population assignment (recombinant genotypes) increased from 10% in 2005 to 17% in 2007, indicating that trichothecene type became an increasingly unreliable marker of population identity over time.
Yet, the power of population assignment approaches is fundamentally linked to the underlying reference population database.
We conducted the analysis according to the admixture model and without any prior population assignment.
The relative contribution of SNP to population assignment was estimated using the informativeness metric In [38].
Together, this demonstrated a subset of markers characterised by high AR and low pAR can be used for population assignment.
To identify marker attributes important for successful population assignment, the distribution of both allelic richness and private allele richness was compared between marker panels (Figure S2).
Population assignment analyses based on these parameters may serve as useful methods for delimiting the early stages of lineage divergence [18], [38].
