title: Non-equilibrium estimates of gene flow inferred from nuclear genealogies suggest that Iberian and North African wall lizards (Podarcis spp.) are an assemblage of incipient species.
abstract: BACKGROUND
  The study of recently-diverged species offers significant challenges both in the definition of evolutionary entities and in the estimation of gene flow among them. Iberian and North African wall lizards (Podarcis) constitute a cryptic species complex for which previous assessments of mitochondrial DNA (mtDNA) and allozyme variation are concordant in describing the existence of several highly differentiated evolutionary units. However, these studies report important differences suggesting the occurrence of gene flow among forms. Here we study sequence variation in two nuclear introns, beta-fibint7 and 6-Pgdint7, to further investigate overall evolutionary dynamics and test hypotheses related to species delimitation within this complex.
  
  
  RESULTS
  Both nuclear gene genealogies fail to define species as monophyletic. To discriminate between the effects of incomplete lineage sorting and gene flow in setting this pattern, we estimated migration rates among species using both FST-based estimators of gene flow, which assume migration-drift equilibrium, and a coalescent approach based on a model of divergence with gene flow. Equilibrium estimates of gene flow suggest widespread introgression between species, but coalescent estimates describe virtually zero admixture between most (but not all) species pairs. This suggests that although gene flow among forms may have occurred the main cause for species polyphyly is incomplete lineage sorting, implying that most forms have been isolated since their divergence. This observation is therefore in accordance with previous reports of strong differentiation based on mtDNA and allozyme data.
  
  
  CONCLUSIONS
  These results corroborate most forms of Iberian and North African Podarcis as differentiated, although incipient, species, supporting a gradual view of speciation, according to which species may persist as distinct despite some permeability to genetic exchange and without having clearly definable genetic boundaries. Additionally, this study constitutes a warning against the misuse of equilibrium estimates of migration among recently-diverged groups.
authors.affiliation: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal. catarina@mail.icav.up.pt
authors.forename: Catarina
authors.initials: C
authors.lastname: Pinho
authors.forename: D James
authors.initials: DJ
authors.lastname: Harris
authors.forename: Nuno
authors.initials: N
authors.lastname: Ferrand
mesh_terms: D000352:Africa, Northern; D000483:Alleles; D025041:Animal Migration; D000818:Animals; D017931:DNA Primers; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D051456:Gene Flow; D049810:Genetic Speciation; D014644:Genetic Variation; D005876:Gibraltar; D006239:Haplotypes; D016013:Likelihood Functions; D008116:Lizards / Q000145:classification / Q000235:genetics*; D021141:Nucleic Acid Amplification Techniques; D010802:Phylogeny; D011174:Portugal; D017422:Sequence Analysis, DNA; D013030:Spain
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial