AbstractAimOceanic islands have often been colonized by small groups of individuals dispersing from the nearest mainland, giving rise to insular populations characterized by locally adapted phenotypes and low genetic diversity. Alternatively, due to past geo‐climatic changes, the present‐day distribution of the species may not correspond to that found at the time of the original colonization so that the current mainland distribution may not include the original source area, leading to erroneous assumptions regarding colonization history. Here, we use patterns of genetic variation to evaluate alternative colonization scenarios of an insular passerine in the Canary Islands.LocationLa Palma (Canary Islands), Northern Africa and the Iberian Peninsula.TaxonRed‐billed chough (Pyrrhocorax pyrrhocorax).MethodsWe use phylogeographical and coalescent analyses of mitochondrial DNA sequences and 10 microsatellite loci, together with Bayesian demographic modelling, to determine whether choughs on the island of La Palma originate from (a) present‐day populations in Iberia, (b) present‐day populations in the mountains of inland Morocco or (c) former populations in coastal Morocco, where suitable habitat existed in the past.ResultsBoth the mitochondrial and nuclear datasets indicate that the chough population on La Palma is genetically well differentiated from those in Iberia and Morocco, and that La Palma choughs are more closely related to choughs in Iberia than to those in Morocco. Genetic diversity in La Palma is lower than that of mainland populations, but shows no evidence of past bottlenecks. The best supported demographic model to explain the origin of La Palma choughs that is congruent with both genetic datasets includes a ‘ghost’ population closely related to Iberia, from which the insular population diverged within the last 30,000 years.Main conclusionsOur results are most consistent with the existence of a former connection between La Palma and Iberia along the North African coast, when suitable habitat was found there. Subsequent desertification of these coastal areas led to local extinctions that restricted gene flow between Iberia and the islands, promoting genetic differentiation. Our results provide a counterintuitive solution to a biogeographical enigma, and could help resolve the colonization history of other systems with similarly complex climatic pasts.
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