Results
Phylogenomic analyses
Multidimensional scaling (MDS) plots based on a distance matrix
generated in ngsdist of 2807 of the most informative SNPs
reveal differentiation between global samples, especially along the
first and section coordinate axes (Figure 3 ). Genetic
differentiation among individuals in each of the 50 populations detected
in our SNP data based on MDS plots was low as expected for a selfing
plant. Six distinct genotype groups (groups I – VI) are clearly
distinguishable. All individuals collected from the same population are
genetically uniform such that they form part of the same genotype group
except in the case of Denmark and Alaska, where individuals are split
between two different groups and/or include a few outlying individuals.
Some of the closest geographic populations sampled from the native range
were resolved in different groups (i.e. France1 belongs to group I and
France2 belongs to group II; Iran1 belongs to group IV and Iran2 belongs
to group II). From left to right in Figure 3, the first genotype group
(group I) includes populations from France1, Iceland, Ireland, Denmark
(in part), Russia, Ukraine, North Dakota (USA), Washington (USA), New
Brunswick (CAN), and New Zealand. The second (group II) includes
France2, England, Netherlands, Denmark (majority of samples), Sweden,
Norway, Finland, Estonia, Italy, Turkey, Iran2, Greenland, and Alberta
(CAN), Colorado (USA), Ontario (CAN), Vancouver (CAN), Chicago (USA),
Newfoundland (CAN), and Alaska (USA, majority of samples). These two
genotype groups primarily consist of populations that originate above
the 35–40o N latitude range (except for New Zealand;Figure 4b ). Individuals collected from Yukon (CAN) form their
own genotype group (group III). Populations from Japan, South Korea,
Iran1, California (USA), and the remaining individuals from Alaska form
a fourth group (group IV). A fifth genotype group (group V) consists of
populations from Spain (Spain1, Spain2), Greece, Gran Canaria, Morocco,
Brazil. The final group (group VI) consists of populations from
Portugal, Egypt, Tenerife, South Africa, Australia (Melbourne and
Perth), Peru, Chile, Hawaiʻi (USA) and Florida (USA). Populations from
groups V and VI all occur below the 35–40o N latitude
range.
Demographic history &
admixture
Shared ancestry was estimated on genotype likelihoods using 7594 SNPs in
ngsadmix for values of K (ancestral populations) between
two and 12, and results for value K =3 and K =8 are
illustrated as a structure graph in Figure 4a . The colours
represent estimated shared ancestry for all sampled populations for each
value of K . Each population comprised 6 – 10 individuals for
which genotyping was performed. Results for additional values ofK are shown in Supplementary Materials. At a K value of 3,
populations from eastern Asia (Japan, South Korea), Yukon, Alaska (in
part), California, and Iran1 comprise of similar ancestry components.
Populations from North America (except for Florida), Iceland, Greenland,
and New Zealand share ancestry with north-central and eastern Europe and
western Asia (Russia, Turkey, Iran2). Populations from South America,
Florida, Hawaiʻi, Africa, and Australia share ancestry with southern
European populations (Figure 4a ). Individual populations from
both introduced and native ranges are very homogenous such that very
little admixture is seen within each population, except for populations
from Alaska, California, and New Zealand. The population from New
Zealand, even at the lowest K value (K = 2), shows more
admixture than other populations, and although individuals from New
Zealand share most of their ancestry with populations from Northern
Europe and North America, there is evidence of admixture with lineages
from Southern Europe, South America, Hawaiʻi, Africa, and Australia.
At a K value of 6, the groupings of shared ancestry resemble the
groupings seen in the MDS plot (Figure 3 ) and therefore
represent a likely ancestry scenario to base discussions on. Two notable
differences are found here compared to the MDS plot. First, Japan and
South Korea are inferred to have a different ancestry than do California
and Iran1 further splitting group IV as shown in the MDS plot. Secondly,
populations belonging to groups V and VI in the MDS plot are not split
into unique ancestries. Only three of the 50 populations sampled
(Denmark, Alaska and New Zealand) showed signs of admixture between two
groups at this value of K .
Population splits and migration
The maximum likelihood tree resulting from the treemix analyses
(Figure 5 ) shows a pattern similar to the genotype groups seen
under MDS plots and ngsadmix results. The three most basal
groups are similar to the groupings seen in admixture analyses forK =3, except for the positions of California and Iran which are
shown to be sister to genotype groups V and VI (occurring below the
35–40o N latitude range) rather than more closely
related to Japan, South Korea and Yukon. Our treemix results
suggest that geneflow occurred between most of the genotype groups. Of
the four migration events modelled, the strongest migration weight
involves geneflow between populations from Alberta to populations in
North Dakota (genotype group I to group II). The other migration events
inferred include migration from Spain2 to New Zealand (genotype group V
to group II), Yukon to Ukraine and Russia (genotype group III to group
I), and Spain1 to Iran2 (genotype group V to group I).