Sampling locations and flower colour variation in Lantana.

(a) thirty-six locations were sampled across different biogeographic regions in India. (b) Flower colour variants used in the study. The names are given based on the variation within an inflorescence. i - White-pink, ii - Yellow-pink, iii - orange, iv - Yellow-pink-b, v - Yellow-pink-c, vi - Reddish-pink, vii - pink, viii - yellow-orange, ix - yellow-orange-b, x – Yellow-dark-pink a, xi - Yellow-dark-pink b.

Schematics of the populations modelled in the SLiM simulations.

The simulations begin with a single population of 100 individuals, which expands exponentially until reaching a carrying capacity of 10,000 individuals. At generation 20,000 two new invasive populations are founded by 10 individuals each. All three populations then evolve independently for an additional 200 generations.

Population structure of Lantana in India.

a) Genetic ancestry assignment using ADMIXTURE programme. Ancestry fractions for K = 4, K = 8 and K = 11 are given with clusters arranged by flower colour variants. b) PCA of all the 359 samples. c) PCA excluding nine samples from northeast India. Individuals are coloured based on their geographic origin from north (green) to south (brown) of India. d) Phylogenetic network showing different lineages associated with flower colour, lineages are coloured based on the flower colour.

Genomic signatures indicating high inbreeding in Lantana

a) Nei’s genetic distance among all the individuals. Nine samples form northeast Indian are genetically most distinct. b) Inbreeding coefficient (F). c) Proportion of heterozygous sites per individual.

Evidence supporting the predominance of self-fertilization in Lantana.

(a) Best-supported demographic model inferred using fastsimcoal2. Pop1 and Pop2 represent distinct flower colour lineages, with arrows indicating inferred gene flow. (b) Graph showing results of the bagging experiment. (c) Individual-based genetic simulation results showing putative patterns of genetic diversity in invasive plants under different assumed mating systems and propagule pressure (i) Heterozygosity (ii) and nucleotide diversity (iii) under different mating systems in ‘native’ and ‘invasive’ populations founded by 10, 100 and 1000 individuals. c) FST between ‘native’ and ‘invasive populations’ under different simulated mating systems and propagule pressure. (iv) FST between two simulated ‘invasive populations’ under different mating systems and propagule pressure.

Optimum number of clusters using Evanno’s delta K method.

PCA based on flower colour of Lantana individuals in India.

Individuals with similar flower colours are coloured similarly in the plot. The flower colour of some of the samples was unknown.

PCA of 50 randomly selected individuals from the simulation scenarios.

P1 is the simulated native population and P2 and P3 are the simulated invasive populations. a) PCA of cross-fertilizing individuals simulated b) PCA of self-fertilizing individuals simulated

Isolation by distance analysis showing a weak correlation between genetic and geographic distance.

Fastsimcoal2 simulation scenarios.

Different flower-colour lineages were simulated with divergence occurring either before or after the introduction, with or without migration. The period approximately from 1600 to 1800 represents the bottleneck associated with introduction to other regions. SplTm denotes the split time, while arrows indicate migration events. TBOT and TENDBOT represent the start and end of the bottleneck, respectively.

Selected Fastsimcoal scenario for yellow-pink and white-pink.

Proportions of cluster assignment for each flower colour type at K = 11.

Cluster assignments are shown for the different flower colour types: (a) white–pink, (b) orange, (c) yellow–pink, (d) pink, (e) yellow–orange, and (f) reddish–orange. The x-axis represents clusters, and the y-axis represents assignment proportions.

Sampling locations.

FST between different populations of Lantana in India.

AIC values for alternative demographic scenarios tested for both flower colour combinations.

Estimated demographic parameters under the Sim8 scenario for the orange and white–pink morphs.

TBOT – Start of bottleneck backward in time, TENBOT – end of bottleneck, SplTm – Split time, MIG21 – Migration from 2 to 1, MIG12 – Migration form 1 to 2.

Summary statistics for the MANOVA.