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On the basis of morphological differences, three subspecies of Black-tailed Godwit ( Limosa limosa ) have been recognized ( L. l. limosa, L. l. islandica  and  L. l. melanuroides ). In previous studies mitochondrial DNA (mtDNA) sequence data showed minimal genetic divergence between the three subspecies and an absence of sub-structuring within  L. l. limosa . Here, population genetic structure and phylogeographic patterns have been analyzed using COI, HVR1 and HVR2 mtDNA sequence data as well as 12 microsatellite loci (nuDNA). The nuDNA data suggest genetic differentiation between  L. l. limosa  from Sweden and The Netherlands, between  L. l. limosa  and  L. l. islandica , but not between  L. l. limosa  and  L. l. melanuroides . However, the mtDNA data were not consistent with the nuDNA pattern. mtDNA did support a split between  L. l. melanuroides  and  L. l. limosa / L. l. islandica  and also demonstrated two  L. l. limosa  haplotype clusters that were not geographically isolated. This genetic structure can be explained by a scenario of isolation of  L. l. melanuroides  from  L. l. limosa  in Beringia during the Last Glacial Maximum. During the Pleistocene separation of  L. l. islandica  from  L. l. limosa  occurred, followed by colonization of Iceland by the  L. l. islandica  during the Holocene. Within  L. l. limosa  founder events, followed by population expansion, took place during the Holocene also. According to the patterns observed in both markers together and their geographic separation, we propose that the three traditional subspecies indeed represent three separate genetic units.

Patterns in Nuclear and Mitochondrial DNA Reveal Historical and Recent Isolation in the Black-Tailed Godwit (Limosa limosa)