**6. Concluding remarks**

**5.4. Perspectives and future work**

PopART [74].

250 Selected Studies in Biodiversity

Previous studies have demonstrated that a consensus about the integrity of the taxa of *Alstroemeria* is far from being reached, as different patterns of differentiation may difficult to be elicited separately. In this sense, molecular markers have provided a natural framework to contextualize their evolutionary process, reconciling discordance observed from different character sources. Nonetheless, despite of their utility, molecular markers are not exempt of limitations that should be addressed in subsequent studies. One of the main limitations to reach a robust taxonomic hypothesis is the recurrent difficulty to obtain consistent molecular markers adaptable enough for interspecific and intraspecific analyses. These difficulties arise from the extraordinary large and complex genomic architecture of *Alstroemeria*, which is likely comprised of a large proportion of repetitive DNA (18–34 pg.) [17]. Our experience suggests that most nuclear markers tend to recurrently fail to retrieve single and readable copies through recurrent Sanger sequencing techniques, especially for the Internal Transcribed Spacer or ITS. Similarly, fragment analyses also exhibit levels of difficulties for consistent scoring, since the effect that

**Figure 12.** Haplotype network inferred with trnL-F chloroplast spacer for individuals sampled from population of *A. ligtu* species complex. Network was constructed under parsimony criteria with TCS [73], as implemented in PopART.

**Figure 11.** Haplotype network inferred with trnL-F chloroplast spacer for individuals sampled from population of *A. magnifica* species complex. Network was constructed under parsimony criteria with TCS [73], as implemented in

> Genetic divergence and population structure estimated with AFLPs and ISSR, have demonstrated the importance of molecular markers for conservation purposes in *Alstroemeria*. Integrative use of molecular data with other source of evidence (morphology, cytology and morphometry) give a best interpretation of lineage divergence with better argumentation for taxonomic delimitation in species complexes of *Alstroemeria*. Due to the high proportion of species complex in genus *Alstroemeria* in Chile, is necessary to carry out phylogenetic studies including the most infraspecifc taxa and more representative sampling, in addition with a major representation of the genome in the analyses. More efforts are needed in producing more stable molecular markers, in order to further implement integrative analyses. In this sense, it is likely that NGS will play a pivotal role helping to overcome present limitations of molecular work in *Alstroemeria*.
