Concordance of Nuclear and Mitochondrial DNA Markers in Detecting a Founder Event in Lake Clark Sockeye Salmon

Genetic bottleneck effects can reduce genetic variation, persistence probability, and evolutionary potential of populations. Previous microsatellite analysis suggested a bottleneck associated with a common founding of sockeye salmon Oncorhynchus nerka populations of Lake Clark, Alaska, about 100 to 400 generations ago. The common founding event occurred after the last glacial recession and resulted in reduced allelic diversity and strong divergence of Lake Clark sockeye salmon relative to neighboring Six Mile Lake and Lake Iliamna populations. Here we used two additional genetic marker types (allozymes and mtDNA) to examine these patterns further. Allozyme and mtDNA results were congruent with the microsatellite data in suggesting a common founder event in Lake Clark sockeye salmon and confirmed the divergence of Lake Clark populations from neighboring Six Mile Lake and Lake Iliamna populations. The use of multiple marker types provided better understanding of the bottleneck in Lake Clark. For example, the Sucker Bay Lake population had an exceptionally severe reduction in allelic diversity at microsatellite loci, but not at mtDNA. This suggests that the reduced microsatellite variation in Sucker Bay Lake fish is due to consistently smaller effective population size than other Lake Clark populations, rather than a more acute or additional bottleneck since founding. Caution is urged in using reduced heterozygosity as a measure of genetic bottleneck effects because stochastic variance among loci resulted in an overall increase in allozyme heterozygosity within bottlenecked Lake Clark populations. However, heterozygosity excess, which assesses heterozygosity relative to allelic variation, detected genetic bottleneck effects in both allozyme and microsatellite loci

Data from: Genetic consequences of a century of protection: serial founder events and survival of the little spotted kiwi (Apteryx owenii)

We present the outcome of a century of post-bottleneck isolation of a long-lived species, the little spotted kiwi (Apteryx owenii, LSK) and demonstrate that profound genetic consequences can result from protecting few individuals in isolation. LSK were saved from extinction by translocation of five birds from South Island, New Zealand to Kapiti Island 100 years ago. The Kapiti population now numbers some 1200 birds and provides founders for new populations. We used 15 microsatellite loci to compare genetic variation among Kapiti LSK and the populations of Red Mercury, Tiritiri Matangi and Long Islands that were founded with birds from Kapiti. Two LSK native to D'Urville Island were also placed on Long Island. We found extremely low genetic variation and signatures of acute and recent genetic bottleneck effects in all four populations, indicating that LSK have survived multiple genetic bottlenecks. The Long Island population appears to have arisen from a single mating pair from Kapiti, suggesting there is no genetic contribution from D'Urville birds among extant LSK. The Ne/NC ratio of Kapiti Island LSK (0.03) is exceptionally low for terrestrial vertebrates and suggests that genetic diversity might still be eroding in this population, despite its large census size

Microsatellite genotypes for LSK in Genepop format

Genotypes of 156 LSK at 21 microsatellite markers ready for use with Genepop or to be converted into another popgen file format. Samples are divided by population and filial group

Data from: Cryptic inbreeding depression in a growing population of a long-lived species

Genetic effects are often overlooked in endangered species monitoring, and populations showing positive growth are often assumed to be secure. However, the continued reproductive success of a few individuals may mask issues such as inbreeding depression, especially in long-lived species. Here, we test for inbreeding depression in little spotted kiwi (Apteryx owenii) by comparing a population founded with two birds to one founded with 40 birds, both from the same source population and both showing positive population growth. We used a combination of microsatellite genotypes, nest observations and modelling to examine the consequences of assessing population viability exclusively via population growth. We demonstrate (i) significantly lower hatching success despite significantly higher reproductive effort in the population with two founders; (ii) positive growth in the population with two founders is mainly driven by ongoing chick production of the founding pair; and (iii) a substantial genetic load in the population founded with two birds (10–15 diploid lethal equivalents). Our results illustrate that substantial, cryptic inbreeding depression may still be present when a population is growing, especially in long-lived species with overlapping generations

MLH values

Standardised multilocus heterozygosity for 156 LSK calculate in Rhh for R. These values were used to calculate our double standardised measure of heterozygosity to create figure 2 in the manuscript

Raw hatching success data for LSK

Raw hatching success data for 33 LSK tracked over two seasons for reproductive effort and hatching success

Apteryx owenii_microsatellite_genotypes_April 2013

Apteryx owenii_microsatellite_genotypes_April 201

Ancient DNA Analyses Reveal Contrasting Phylogeographic Patterns amongst Kiwi (<em>Apteryx</em> spp.) and a Recently Extinct Lineage of Spotted Kiwi

<div><p>The little spotted kiwi (<em>Apteryx owenii</em>) is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (<em>A. mantelli</em>, <em>A. rowi</em> and <em>A. australis</em>), with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (<em>A. haastii</em>) formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species) survived on the South Island mainland until more recently than previously thought.</p> </div

Figure 1

<p>A. Distribution of spotted kiwi haplotypes. The current distribution of great spotted kiwi is depicted in green. Little spotted kiwi presently (2012) occur on several predator-free offshore islands and a wildlife sanctuary on the mainland (not shown); all derive from transfers from Kapiti Island or D’Urville Island (little spotted kiwi have been removed from the latter). Little spotted kiwi haplotypes are represented by circles; great spotted kiwi samples are indicated by diamonds. Only the approximate position of the sample from ‘West Coast, South Island’ (museum number AV25141) is indicated on the map because of the imprecision of its recorded locality. A star indicates the position of the sample (AV17079) from which a partial DNA sequence identical to the control region of haplotype A was obtained. B. Distribution of brown kiwi haplotypes. The current distribution of North Island brown kiwi is shown in blue and their haplotypes are shown as pentagons. The distribution of rowi is shown in red and their haplotypes as triangles. The distribution of tokoeka is shown in grey and tokoeka haplotypes are shown as squares. In both maps the location names of ancient samples are shown in bold and underlined. C. Midpoint-rooted Bayesian phylogeny of the expanded sample set which included all spotted and brown kiwi samples and all loci (missing loci were coded as missing data). Numbers above the branches represent posterior probabilities (PP), MP and ML bootstrap (BS) values, respectively. Only PP>0.70 and BS>50% are shown.</p