Genetic diversity and gene flow in a rare New Zealand skink despite fragmented habitat in a volcanic landscape

Abstract

Anthropogenic habitat fragmentation often restricts gene flow and results in small populations that are at risk of inbreeding. However, some endangered species naturally occupy patchy habitat where local population extinction and recolonization are normal. We investigated population fragmentation in the range-restricted New Zealand small-scaled skink (Oligosoma microlepis), documenting changes in habitat occupancy and analyzing mitochondrial, microsatellite, and morphological variation sampled across the geographical range of the species (approximately 100 km2). Small-scaled skinks have a strong preference for rocky outcrops that exist in a mosaic of other habitat types. A metapopulation structure was indicated by both local extinction and colonization of new sites. We found relatively high mtDNA nucleotide site diversity within this narrow range (π = 0.004; 16S), evidence of inter-patch gene flow, and no statistical support for inbreeding. Gene flow was limited by geographical distance, although the existence of pasture between habitat patches apparently has not prevented skink dispersal. Generalized linear models indicated an association between body size and location suggesting a local environmental influence on phenotype. Prior to human-induced habitat modification, native forest probably separated preferred sites and, less than 2000 years ago, volcanic activity devastated much of the area currently occupied by O. microlepis. This skink appears able to re-establish populations if other human-linked factors such as agricultural intensification and introduced predators are limited. Although in contrast to expectations for a scarce and localized species living in a highly modified landscape, this lizard may have previously adapted to a dynamic, mosaic environment mediated by volcanism.