Allopolyploidy is a significant mechanism of plant speciation, and many allopolyploid species have arisen recurrently. However, the probability that allopolyploidization between the same two parental species may lead to the origin of different taxa has received little attention. Here we used a new progenitor-specific amplicon sequencing method to demonstrate the independent origins of two yarrow species, Achillea alpina and A. wilsoniana, via allotetraploidy from the same diploid progenitor species pair, A. acuminata and A. asiatica. Based on the sequences of 17 nuclear genes from 21 wild populations of the four Achillea species investigated, a clear view of  genetic structure and demographic history was obtained with each species. Significant genetic differentiation was evident between the two tetraploid species. Two genetically distinguishable groups were detected within one of the progenitor, A. acuminata, and ancestors belonging to those two groups contributed to the two tetraploid species, respectively. Excluding fixed heterozygosity, we detected extremely low genetic diversity in many populations of both tetraploid species. Approximate Bayesian computation indicated that both tetraploid species originated before the Last Glacial Maximum, and nearly all diploid lineages went through population declines after the allopolyploidization events. Our study demonstrates that independent allopolyploidization events between the same Achillea parental species have generated two genetically and ecologically distinct taxa.

• SNP
  • SNP statistics based on transcriptomes of three species
  • SNP.xlsx
• structure_c
  • STRUCTURE input file for the c-subset
  • structure_Hap17_c.txt
• structure_s
  • STRUCTURE input file for the s-subset
  • structure_Hap17_s.txt
• allele_types
  • allele types/sequences for each fragment
  • allele types.fas
• allele_statistics
  • allele statistics for each amplicon
  • allele statistics.xlsx
• resample_SNP_c
  • 100 resampled SNP files for the c-subset
  • resample_SNP_c.rar
• resample_SNP_s
  • 100 resampled SNP files for the s-subset
  • resample_SNP_s.rar
• alp_unigene
  • unigenes in A. alpina from transcriptome assembly
  • alp-unigene.fas
• abc_c -
  • DIYABC input file (DNA sequence file of introns) for the c-subset
  • abc_c.mss
• abc_s
  • DIYABC input file (DNA sequence file of introns) for the s-subset
  • abc_s.mss
• acu_unigene
  • unigenes in A. acuminate from transcriptome assembly
  • acu-unigene.fas
• asi_unigene
  • unigenes in A. asiatica from transcriptome assembly
  • asi-unigene.fas