Genetic Exchangeability
Following the Bond and Stockman (2008) flowchart for delimiting cohesion
species, we first established a “basal lineage” starting point,
resulting in five lineages. Lineage name designations were based on
clade labels from Hendrixson and Bond (2005b; see Figure 2): A.
microunicolor and four lineages within A. unicolor (A, B1, B2,
and B3). We assessed the potential for gene flow (i.e. genetic
exchangeability) between sister lineages by evaluating the distributions
of these lineages (Figure 1).
To help elucidate the potential for gene flow, several clustering
analyses were performed. STRUCTURE v 2.3.4 (Pritchard et al., 2000) was
run with several data matrices of unlinked SNPs for 1,000,000
generations and 100,000 burn-in using the admixture model featuring K
values ranging from 1-10, with five replicate runs for each K value. The
package pophelper (Francis, 2017) in R v.3.5.3 (R Core Team, 2019) was
used to calculate the optimal K value via the Evanno method of
calculating 𝚫K (Evanno, Regnaut, and Goudet 2005) as well as view the
output (Figure 3a). In addition to STRUCTURE, we also used the R package
adegenet (Jombart, 2008; Jombart & Ahmed, 2011) to perform a principal
components analysis (dudi.pca function) and visualize the clustering of
each lineage (Figure 3b). Also, an unsupervised machine learning
approach, specifically a Variational Autoencoder (VAE), was implemented
to provide another clustering algorithm (Figures 3c & 3d; for details
see Derkarabetian et al. 2019). This approach, which relies on the
inherent structure within the data for clustering individuals,
alleviates the need for a priori hypotheses of species number, level of
divergence, and any population parameters. VAEs, derived from Bayesian
probability theory, provide relatively clear visualization for assessing
cluster uncertainty due to the standard deviation around
samples/clusters (Derkarabetian et al., 2019).
In cases of allopatric lineages, we considered the lineages isolated and
genetic exchangeability was rejected. However, in cases of sympatric or
parapatric lineages with uncertainty of whether a barrier to gene flow
is present, we tentatively accept genetic exchangeability unless the
clustering analyses indicate separate clusters. Because cohesion species
can be rejected by either not being genetically exchangeable orecologically interchangeable, these lineages were also tested for
ecological interchangeability.