Postglacial expansion and not human influence best explains the population structure in the endangered kea (Nestor notabilis)

Abstract

Inferring past demography is a central question in evolutionary and conservation biology. It is, however, sometimes challenging to infer the processes that shaped the current patterns of genetic variation in endangered species. Population substructuring can occur as a result of survival in several isolated refugia and subsequent recolonization processes or via genetic drift following a population decline. The kea (Nestor notabilis) is an endemic parrot widely distributed in the mountains of the South Island of New Zealand that has gone through a major human-induced population decline during the 1860s-1970s. The aims of this study were to understand the glacial and postglacial history of kea and to determine whether the recent population decline played a role in the shaping of the current genetic variation. We examined the distribution of genetic variation, differentiation and admixture in kea using 17 microsatellites and the mitochondrial control region. Mitochondrial data showed a shallow phylogeny and a genetic distinction between the North and South of the range consistent with the three genetic clusters identified with microsatellite data. Both marker types indicated an increase in genetic isolation by geographic distance. Approximate Bayesian Computation supported a scenario of postglacial divergence from a single ancestral glacial refugium, suggesting that the contemporary genetic structure has resulted from recolonization processes rather than from a recent population decline. The recent evolutionary origin of this genetic structure suggests that each genetic cluster does not need to be considered as independent conservation units.

Strong isolation by distance argues for separate population management of endangered blue duck (Hymenolaimus malacorhynchos)

“…Because of sampling gaps between regions that correspond to genetic clusters, and the longitudinal distribution of these clusters within the SI, we cannot exclude the possibility of clinal genetic variation rather than discrete genetic units (STRUCTURE analysis has known limitations in the presence of allelic clines; Pritchard et al 2000). Indeed, clinal genetic variation is supported by a Number of pairwise differences Dussex et al 2014), which likely represent a history of postglacial expansion out of a single refugium followed by extensive gene flow between populations in this highly dispersive taxon. Overall, our analyses suggest that blue duck dispersal between catchments, and on wider geographic scales, is greater than what had been assumed for many years.…”

Ancient and Contemporary DNA Reveal a Pre-Human Decline but No Population Bottleneck Associated with Recent Human Persecution in the Kea (Nestor notabilis)

“…We utilized a contemporary dataset from birds caught between 2010 and 2012 comprising 91 mitochondrial (mtDNA) control region (CR) sequences and 410 nuclear microsatellite genotypes (17 microsatellite loci) as described in Dussex et al [45]. Additionally, historical skins (n = 15) with robust locality data, and Late Glacial (10–14 kya) and Holocene fossil bones (< 11.6 kya; n = 4) [31, 47] from across the geographic range of kea were obtained from New Zealand and overseas museum collections (Table 1, Fig.…”

“…Historical samples were genotyped for 17 microsatellite loci [45] using cycling conditions outlined in [51] with an increase in the number of cycles from 8 to 12 and from 25 to 30. All samples were independently amplified five times in order to decrease the chances of allelic dropout [52].…”

“…and the same PCR conditions described in Dussex et al [45] but with an increase in cycle number to 60.…”

“…Previous results have shown that despite its strong flying capabilities, the kea is subdivided into three distinct genetic clusters and that this population structure is most likely the result of postglacial recolonization processes but not a recent human-induced fragmentation [45]. Kea populations might also have fluctuated through time in response to climate variations during the Pleistocene and Holocene as has been shown in many other New Zealand species [7, 46].…”