Little Spotted Kiwi (LSK; Apteryx owenii) have the lowest genetic diversity of five currently recognised kiwi species apparently due to a bottleneck when at most five individuals were translocated to Kapiti Island in 1912. Ancient DNA analyses show that LSK also had the lowest genetic diversity of kiwi species historically, possibly due to population bottlenecks during Pleistocene glaciation. We compare genetic diversity between LSK from Kapiti Island (extant), D’Urville Island (extinct) and the South Island of mainland New Zealand (extinct) at 495 bp of the mitochondrial control region (mtDNA) and 15 nuclear microsatellite loci (nDNA). Despite higher sample sizes in extant (n = 31 mtDNA, 97 nDNA) than recently extinct (n = 10 mtDNA, 9 nDNA) populations, extant LSK have at least 78% fewer mtDNA haplotypes and 52% fewer microsatellite alleles than recently extinct LSK. Extant LSK were strongly divergent from historical LSK for both mtDNA and nDNA (F_ST = 0.237 to 0.480), but showed greatest similarity with historical samples from Fiordland near the putative source population of Kapiti founders. Microsatellite data suggest that Kapiti LSK could have arisen from as few as three birds and our mtDNA data show that at least two of the founders were female. Our results indicate that substantial genetic diversity has been lost with the recent extinctions of remnant populations. Locating and protecting any last surviving individuals in presumed extinct populations will require intensive conservation efforts, but could also provide an invaluable source of genetic diversity for the species.

Please see the Methods sections of the associated peer-reviewed journal article for this information.

Please see the associated Readme for file (Apteryx owenii_microsatellite_genotypes_July2020) for this information.