**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/20/24/ 6130/s1.

**Author Contributions:** Conceptualization, S.R.S., V.F.O.M., and A.M.V.; methodology, S.R.S., A.M.V., and D.G.P., V.F.O.M., T.P.M., H.A.P., and E.J.M.; software, S.R.S., A.M.V., V.F.O.M., and D.G.P.; validation, S.R.S., D.G.P., V.F.O.M., and A.M.V.; formal analysis, S.R.S., A.M.V., V.F.O.M., and D.G.P.; investigation, S.R.S., A.M.V., V.F.O.M., and D.G.P.; resources, S.R.S., V.F.O.M., T.P.M., E.J.M., and A.M.V.; data curation, S.R.S., V.F.O.M. and A.M.V.; writing—original draft preparation, S.R.S., A.M.V., and V.F.O.M.; writing—review and editing, S.R.S., A.M.V., D.G.P., T.P.M., H.A.P., B.J.P., and E.J.M.; visualization, S.R.S., V.F.O.M., A.M.V., and T.P.M.; supervision, V.F.O.M. and A.M.V.; project administration, S.R.S., V.F.O.M., and A.M.V.; funding acquisition, V.F.O.M., A.M.V., and T.P.M.

**Funding:** This research was funded by FAPESP—Fundação de Amparo à Pesquisa do Estado de São Paulo (Proc. #2013/05144-0, #2013/25164-6, #2018/02285-6) and in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES), Finance Code 001 and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the fellowships (Bolsa de Produtividade—Grant # 312908/2018-0 for VFOM and #302599/2016-9 for AMV).

**Acknowledgments:** We thank Cristine Gobbo Menezes and all colleagues from the Laboratory of Plant Systematics (Unesp/FCAV) for collaboration in searching for *Utricularia* natural populations and fruitful discussions. We also thank Tiago Santana Balbuena (Unesp/FCAV) for providing the opportunity to use the server to support the analyses.

**Conflicts of Interest:** The authors declare no conflict of interest.

**Ethical Statements:** The *Utricularia amethystina* samples were collected with the SisBio authorization #48516-1, by the Ministério do Meio Ambiente (MMA) and Instituto Chico Mendes de Conservação da Biodiversidade (IGMBio).
