title: Multilocus assessment of phylogenetic relationships in Alytes (Anura, Alytidae).
abstract: With the advent of large multilocus datasets, molecular systematics is experiencing very rapid progress, but important challenges remain regarding data analysis and interpretation. Midwife toads (genus Alytes) exemplify two of the most widespread problems for accurate phylogenetic reconstruction: discerning the causes of discordance between gene trees, and resolving short internodes produced during rapid, successive splitting events. The three species in subgenus Baleaphryne (A. maurus, A. dickhilleni and A. muletensis), the sister group to A. obstetricans, have disjunct and highly restricted geographical ranges, which are thought to result from old vicariant events affecting their common ancestor, but their phylogenetic relationships are still unresolved. In this study we re-address the phylogeny of Alytes with a special focus on the relationships in Baleaphryne with a multilocus dataset including >9000 base pairs of mitochondrial DNA and four nuclear markers (3142bp) in all recognized taxa, including all subspecies of A. obstetricans. Both concatenation and species tree analyses suggest that A. muletensis, endemic to the Balearic island of Mallorca, is the sister taxon to a clade comprising the southeastern Iberian endemic A. dickhilleni and the North African A. maurus. This scenario is consistent with palaeogeological evidence associated with the fragmentation of the Betic-Rifean Massif, followed by the opening of the Strait of Gibraltar. On the other hand, analyses of intraspecific variation in A. obstetricans are inconclusive regarding relationships between major clades and conflict with current subspecific taxonomy.
authors.affiliation: CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, InBIO, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Zoologia e Antropologia - Faculdade de Ciências da Universidade do Porto, 4099-002 Porto, Portugal.
authors.forename: Bruno
authors.initials: B
authors.lastname: Maia-Carvalho
authors.affiliation: CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, InBIO, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
authors.forename: Helena
authors.initials: H
authors.lastname: Gonçalves
authors.affiliation: CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, InBIO, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Zoologia e Antropologia - Faculdade de Ciências da Universidade do Porto, 4099-002 Porto, Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Ferrand
authors.affiliation: CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, InBIO, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM). Ronda de Toledo, s/n, 13005 Ciudad Real, Spain. Electronic address: inigomsolano@gmail.com.
authors.forename: Iñigo
authors.initials: I
authors.lastname: Martínez-Solano
mesh_terms: D000818:Animals; D001001:Anura / Q000145:classification* / Q000235:genetics; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D005819:Genetic Markers; D016013:Likelihood Functions; D019083:Mediterranean Region; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial; D005819:Genetic Markers
keywords: Alytes; Baleaphryne; Concatenation; Multispecies coalescent; Species trees; mtDNA