title: Physalis and physaloids: A recent and complex evolutionary history.
abstract: The complex evolutionary history of the subtribe Physalinae is reflected in the poor resolution of the relationships of Physalis and the physaloid genera. We hypothesize that this low resolution is caused by recent evolutionary history in a complex geographic setting. The aims of this study were twofold: (1) To determine the phylogenetic relationships of the current genera recognized in Physalinae in order to identify monophyletic groups and resolve the physaloid grade; and (2) to determine the probable causes of the recent divergence in Physalinae. We conducted phylogenetic analyses with maximum likelihood (ML) and Bayesian inference with 50 Physalinae species and 19 others as outgroups, using morphological and molecular data from five plastid and two nuclear regions. A relaxed molecular clock was obtained from the ML topology and ancestral area reconstruction was conducted using the DEC model. The genera Chamaesaracha, Leucophysalis, and Physalis subgenus Rydbergis were recovered as monophyletic. Three clades, Alkekengi-Calliphysalis, Schraderanthus-Tzeltalia, and Witheringia-Brachistus, also received good support. However, even with morphological data and that of the DNA of seven regions, the tree was not completely resolved and many clades remained unsupported. Physalinae diverged at the end of the Miocene (∼9.22Mya) with one trend indicating that the greatest diversification within the subtribe occurred during the last 5My. The Neotropical region presented the highest probability (45%) of being the ancestral area of Physalinae followed by the Mexican Transition Zone (35%). During the Pliocene and Pleistocene, the geographical areas where species were found experienced significant geological and climatic changes, giving rise to rapid and relatively recent diversification events in Physalinae. Thus, recent origin, high diversification, and morphological complexity have contributed, at least with the currently available methods, to the inability to completely disentangle the phylogenetic relationships of Physalinae.
authors.affiliation: Instituto de Botánica, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Apartado postal 1-139, CP 45101 Zapopan, Jalisco, Mexico. Electronic address: pilarzamoratavares@gmail.com.
authors.forename: María Del Pilar
authors.initials: MDP
authors.lastname: Zamora-Tavares
authors.affiliation: Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. De las Ciencias s/n, Juriquilla, CP 76230, Del. Sta. Rosa Jáuregui, Querétaro, Mexico. Electronic address: mahinda@uaq.mx.
authors.forename: Mahinda
authors.initials: M
authors.lastname: Martínez
authors.affiliation: Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico. Electronic address: s.magallon@ib.unam.mx.
authors.forename: Susana
authors.initials: S
authors.lastname: Magallón
authors.affiliation: Instituto de Botánica, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Apartado postal 1-139, CP 45101 Zapopan, Jalisco, Mexico. Electronic address: lguzman@cucba.udg.mx.
authors.forename: Laura
authors.initials: L
authors.lastname: Guzmán-Dávalos
authors.affiliation: Instituto de Botánica, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Apartado postal 1-139, CP 45101 Zapopan, Jalisco, Mexico. Electronic address: vargasofelia@gmail.com.
authors.forename: Ofelia
authors.initials: O
authors.lastname: Vargas-Ponce
mesh_terms: D001499:Bayes Theorem; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D014644:Genetic Variation; D010802:Phylogeny; D032321:Physalis / Q000145:classification* / Q000235:genetics*; D013997:Time Factors
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant
keywords: Ancestral area reconstruction; Mexican Transition Zone; Molecular clock; Recent divergence; Solanaceae