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Immunity genes are proposed to be informative about evolutionary processes acting upon introduced populations (e.g., showing signatures of selection). This is because immunity genes are expected to be under pathogen-mediated selection, and this type of selection can be more pronounced when individuals are exposed to new environmental conditions. Here we assessed innate immune genetic diversity, via Toll-like receptors (TLRs), to quantify genetic differentiation between a deliberately introduced population of dunnocks (Prunella modularis) in New Zealand and its source population in the United Kingdom. We also asked whether the introduced population shows signatures of intergenerational and current selection in TLR. We expect intergenerational and current selection patterns because New Zealand dunnocks have been exposed to new environmental conditions following their introduction around the late 1800s, which may have driven pathogen-mediated selection. Counter to our expectation, we found only weak and non-significant genetic differentiation between the introduced and source populations. Further, the levels of genetic differentiation (GST′) found in TLRs were similar to those found in microsatellites across the populations. Dunnocks, in general, have been under strong purifying selection over evolutionary time, but we found little evidence to support signatures of contemporary selection in TLR in the introduced population. Notably, however, we found a statistically significant heterozygosity advantage for males in TLR3, which lends support to possible current selection acting upon the introduced population. Overall, it appears that New Zealand dunnocks have retained a high proportion of the immunogenetic diversity of the source population, and that such diversity has probably been sufficient to defend against the potential pathogens found in New Zealand. Our results may explain—at least in part—why the introduction of dunnocks has been so successful; dunnocks have become one of the most common birds in New Zealand. [ABSTRACT FROM AUTHOR]

In the original publication of the article Evol Ecol 34, 803–820 (2020) we suggested that "Historical records from the Otago Acclimatisation Society indicate that in the Otago region...a total of 185 individuals...were introduced from United Kingdom between 1865 and 1907 (Santos 2012; Santos and Nakagawa 2013)". [ABSTRACT FROM AUTHOR]

The rediscovery of the Takahe Porphyrio hochstetteri in 1948 in the remote mountains of Fiordland, New Zealand, has been described as one of the greatest moments in ornithological history. The subsequent management of the population has become a model for avian recovery programmes, yet questions still remain regarding the population size at the time of, and prior to, its rediscovery. We used 20 microsatellite markers to genotype samples of the three surviving museum specimens (1849-1898) collected prior to the initial declaration of extinction to estimate levels of genetic diversity and effective population size. These estimates were compared with equivalent estimates from DNA samples of three specimens preserved at the time of rediscovery (1949) and with 20 contemporary samples. Using rarefaction simulations to account for the limited sample sizes, the results suggest that only slightly more genetic diversity (allelic diversity and numbers of polymorphic loci) existed in the earliest Takahe sampled and that levels of genetic diversity at the time of rediscovery were very similar to those today. Effective population size estimates showed a similar pattern. Contemporary samples from a widespread congener to Takahe, the Pukeko Porphyrio porphyrio, showed consistently higher levels of genetic diversity and greater effective population size, even after equivalent rarefaction to the same small sample sizes available for Takahe. It is likely that the population size of Takahe in Fiordland at the time of European arrivals in the 1800s was similar to its current size. These results provide molecular support for the hypothesis that Takahe were common throughout most coastal and eastern parts of the South Island of New Zealand before being hunted to extinction in these regions by early Maori, and persisted as a relatively small and isolated population in Fiordland where they may never have been very common. This is in marked contrast to other New Zealand endemic birds found in Fiordland, such as the Kakapo Strigops habroptilus and several forest passerines, which remained relatively numerous until the time of European arrival before undergoing rapid declines thereafter. [ABSTRACT FROM AUTHOR]

Pedigree analysis has clear benefits for the genetic management of threatened populations through the evaluation of inbreeding, population structure and genetic diversity. The use of pedigrees is usually restricted to captive populations and few examples exist of their exclusive use in managing free-ranging populations. One such example is the management of the takahe (Porphyrio hochstetteri), a highly endangered, flightless New Zealand rail at risk from introduced mammalian predators and habitat loss. During the 1980's and 90's, as part of the takahe recovery programme, birds were translocated from the sole remnant population in Fiordland to four offshore islands from which introduced predators had been eradicated. The subsequent ''island'' population, now numbering 83 and thought to be at carrying capacity, has been closely monitored since founding. Detailed breeding records allow us to analyse the island pedigree, which is up to 7 generations deep. Gene-drop analysis indicated that 7.5% of genetic diversity has been lost over the relatively short timeframe since founding (2.1 generations on average; total genetic founders = 31) due to both a failure to equalise founder representation early on and subsequent disproportionate breeding success (founder equivalents = 12.5; founder genome equivalents = 6.6). A high prevalence of close inbreeding will have also impacted on genetic diversity. Predictions from pedigree modelling suggest that 90% genetic diversity will be maintained for only 12 years, but by introducing a low level of immigration from the Fiordland population and permitting the population to grow, 90% GD could be maintained over the next 100 years. More generally, the results demonstrate the value of maintaining pedigrees for wild populations, especially in the years immediately after a translocation event. [ABSTRACT FROM AUTHOR]

Nineteen polymorphic microsatellite loci were characterized from the endangered takahe ( Porphyrio hochstetteri). Like many of New Zealand's other native avian species, levels of polymorphism were low, with variation detected at only 19 of 110 (17.3%) loci, and most polymorphic loci (78.9%) were diallelic (mean number of alleles = 2.3). Despite these low levels of variation, the microsatellites developed here will be useful for parentage assignment for confirming pedigrees, and investigating relationships between genetic variation, pedigree-based inbreeding and reproductive success in this highly endangered species. [ABSTRACT FROM AUTHOR]

Pathogen outbreaks in the wild can contribute to a population's extinction risk. Concern over the effects of pathogen outbreaks in wildlife is amplified in small, threatened populations, where degradation of genetic diversity may hinder natural selection for enhanced immunocompetence. Beak and feather disease virus (BFDV) was detected for the first time in an island population of red-crowned parakeets (Cyanoramphus novaezelandiae) in 2008 on Little Barrier Island (Hauturu-o-Toi) of New Zealand. By 2013, the prevalence of the viral infection had significantly decreased within the population. We tested whether the population of red-crowned parakeets showed a selective response to BFDV, using neutral microsatellite and two immunity-associated genetic markers, the major histocompatibility complex (MHC) and Toll-like receptors (TLRs). We found evidence for selection at viral-associated TLR3; however, the ability of TLR3 to elicit an immune response in the presence of BFDV warrants confirmation. Alternatively, because red-crowned parakeet populations are prone to fluctuations in size, the decrease in BFDV prevalence over time may be attributed to the Little Barrier Island population dropping below the density threshold for viral maintenance. Our results highlight that natural processes such as adaptation for enhanced immunocompetence and/or density fluctuations are efficient mechanisms for reducing pathogen prevalence in a threatened, isolated population.

Although evidence of inbreeding depression in wild populations is well established, the impact of genetic purging in the wild remains controversial. The contrasting effects of inbreeding depression, fixation of deleterious alleles by genetic drift, and the purging of deleterious alleles via natural selection mean that predicting fitness outcomes in populations subjected to prolonged bottlenecks is not straightforward. We report results from a long-term pedigree study of arguably the world's most inbred wild species of bird: the Chatham Island black robin Petroica traversi, in which conditions were ideal for purging to occur. Contrary to expectations, black robins showed a strong, negative relationship between inbreeding and juvenile survival, yielding lethal equivalents (2B) of 6.85. We also determined that the negative relationship between inbreeding and survival did not appear to be mediated by levels of ancestral inbreeding and may be attributed in part to unpurged lethal recessives. Although the black robin demographic history provided ideal conditions for genetic purging, our results show no clear evidence of purging in the major life-history trait of juvenile survival. Our results also show no evidence of fixation of deleterious alleles in juvenile survival, but do confirm that continued high levels of contemporary inbreeding in a historically inbred population could lead to additional severe inbreeding depression., (© 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.)

The major histocompatibility complex (MHC) is integral to the vertebrate adaptive immune system. Characterizing diversity at functional MHC genes is invaluable for elucidating patterns of adaptive variation in wild populations, and is particularly interesting in species of conservation concern, which may suffer from reduced genetic diversity and compromised disease resilience. Here, we use next generation sequencing to investigate MHC class II B (MHCIIB) diversity in two sister taxa of New Zealand birds: South Island saddleback (SIS), Philesturnus carunculatus, and North Island saddleback (NIS), Philesturnus rufusater. These two species represent a passerine family outside the more extensively studied Passerida infraorder, and both have experienced historic bottlenecks. We examined exon 2 sequence data from populations that represent the majority of genetic diversity remaining in each species. A high level of locus co-amplification was detected, with from 1 to 4 and 3 to 12 putative alleles per individual for South and North Island birds, respectively. We found strong evidence for historic balancing selection in peptide-binding regions of putative alleles, and we identified a cluster combining non-classical loci and pseudogene sequences from both species, although no sequences were shared between the species. Fewer total alleles and fewer alleles per bird in SIS may be a consequence of their more severe bottleneck history; however, overall nucleotide diversity was similar between the species. Our characterization of MHCIIB diversity in two closely related species of New Zealand saddlebacks provides an important step in understanding the mechanisms shaping MHC diversity in wild, bottlenecked populations.

Preserving allelic diversity is important because it provides the capacity for adaptation and thus enables long-term population viability. Allele retention is difficult to predict in animals with overlapping generations, so we used a new computer model to simulate retention of rare alleles in small populations of 3 species with contrasting life-history traits: North Island Brown Kiwi (Apteryx mantelli; monogamous, long-lived), North Island Robins (Petroica longipes; monogamous, short-lived), and red deer (Cervus elaphus; polygynous, moderate lifespan). We simulated closed populations under various demographic scenarios and assessed the amounts of artificial immigration needed to achieve a goal of retaining 90% of selectively neutral rare alleles (frequency in the source population = 0.05) after 10 generations. The number of immigrants per generation required to meet the genetic goal ranged from 11 to 30, and there were key similarities and differences among species. None of the species met the genetic goal without immigration, and red deer lost the most allelic diversity due to reproductive skew among polygynous males. However, red deer required only a moderate rate of immigration relative to the other species to meet the genetic goal because nonterritorial breeders had a high turnover. Conversely, North Island Brown Kiwi needed the most immigration because the long lifespan of locally produced territorial breeders prevented a large proportion of immigrants from recruiting. In all species, the amount of immigration needed generally decreased with an increase in carrying capacity, survival, or reproductive output and increased as individual variation in reproductive success increased, indicating the importance of accurately quantifying these parameters to predict the effects of management. Overall, retaining rare alleles in a small, isolated population requires substantial investment of management effort. Use of simulations to explore strategies optimized for the populations in question will help maximize the value of this effort.., (© 2013 Society for Conservation Biology.)

Toll-like receptors (TLRs) are an ancient family of genes encoding transmembrane proteins that bind pathogen-specific molecules and initiate both innate and adaptive aspects of the immune response. Our goal was to determine whether these genes show sufficient genetic diversity in a bottlenecked population to be a useful addition or alternative to the more commonly employed major histocompatibility complex (MHC) genotyping in a conservation genetics context. We amplified all known avian TLR genes in a severely bottlenecked population of New Zealand's Stewart Island robin (Petroica australis rakiura), for which reduced microsatellite diversity was previously observed. We genotyped 17-24 birds from a reintroduced island population (including the 12 founders) for nine genes, seven of which were polymorphic. We observed a total of 24 single-nucleotide polymorphisms overall, 15 of which were non-synonymous, representing up to five amino-acid variants at a locus. One locus (TLR1LB) showed evidence of past directional selection. Results also confirmed a passerine duplication of TLR7. The levels of TLR diversity that we observe are sufficient to justify their further use in addressing conservation genetic questions, even in bottlenecked populations.