Kristina M. Ramstad

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska.

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six‐mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six‐mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six‐mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six‐mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sockeye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

Radio Tag Retention and Tag-Related Mortality among Adult Sockeye Salmon

Abstract Tag retention and tag-related mortality are concerns for any tagging study but are rarely estimated. We assessed retention and mortality rates for esophageal radio tag implants in adult sockeye salmon Oncorhynchus nerka. Migrating sockeye salmon captured at the outlet of Lake Clark, Alaska, were implanted with one of four different radio tags (14.5 × 43 mm (diameter × length), 14.5 × 49 mm, 16 × 46 mm, and 19 × 51 mm). Fish were observed for 15 to 35 d after tagging to determine retention and mortality rates. The overall tag retention rate was high (0.98; 95% confidence interval (CI), 0.92-1.00; minimum, 33 d), with one loss of a 19-mm × 51- mm tag. Mortality of tagged sockeye salmon (0.02; 95% CI, 0-0.08) was similar to that of untagged controls (0.03 (0-0.15)). Sockeye salmon with body lengths (mid-eye to tail fork) of 585-649 mm retained tags as large as 19 × 51 mm and those with body lengths of 499-628 mm retained tags as small as 14.5 × 43 mm for a minimum of 33 d with no increase in mortali...

Genetic and Phenotypic Evidence of Reproductive Isolation between Seasonal Runs of Sockeye Salmon in Bear Lake, Alaska

Abstract The effective conservation of salmonids requires the recognition and preservation of populations that are diverse in genetic composition and life history. The management of sockeye salmon Oncorhynchus nerka in Bear Lake, Alaska, is based on the presumption that there are two, genetically isolated seasonal runs that exhibit a bimodal escapement pattern. We investigated the genetic composition and life history of the putative early and late runs in two consecutive years. Significant allele frequency differences at six microsatellite loci demonstrate restricted gene flow between the early and late runs (F ST = 0.017). There were also significant, and presumably adaptive, differences between the runs with respect to body weight, somatic weight, ovary weight, and egg size among females after correction to equal body sizes. Further, scale pattern analysis revealed highly significant differences in the growth-at-age patterns of these runs. These results demonstrate that there are significant genetic dif...

Characterisation of class II B MHC genes from a ratite bird, the little spotted kiwi (Apteryx owenii)

Major histocompatibility complex (MHC) genes are important for vertebrate immune response and typically display high levels of diversity due to balancing selection from exposure to diverse pathogens. An understanding of the structure of the MHC region and diversity among functional MHC genes is critical to understanding the evolution of the MHC and species resilience to disease exposure. In this study, we characterise the structure and diversity of class II MHC genes in little spotted kiwi Apteryx owenii, a ratite bird representing the basal avian lineage (paleognaths). Results indicate that little spotted kiwi have a more complex MHC structure than that of other non-passerine birds, with at least five class II MHC genes, three of which are expressed and likely to be functional. Levels of MHC variation among little spotted kiwi are extremely low, with 13 birds assayed having nearly identical MHC genotypes (only two genotypes containing four alleles, three of which are fixed). These results suggest that recent genetic drift due to a species-wide bottleneck of at most seven birds has overwhelmed past selection for high MHC diversity in little spotted kiwi, potentially leaving the species highly susceptible to disease.

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

The little spotted kiwi (Apteryx owenii) is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis), 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 (A. haastii) 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.

Fourteen microsatellite loci cross-amplify in all five kiwi species (Apteryx spp.) and reveal extremely low genetic variation in little spotted kiwi (A. owenii)

We present 14 microsatellite loci that were isolated from little spotted kiwi (LSK, Apteryx owenii). All loci cross-amplify in all kiwi species currently recognized except for one locus in a single species. Little spotted kiwi exhibited lower variation at these loci (mean number of alleles, HE) than other kiwi species, despite the markers having been developed for polymorphism in LSK and a far greater number of LSK genotyped than kiwi of other species. Reliable cross-species amplification and polymorphism make these markers promising new tools for the management of New Zealand’s threatened kiwi.

Effective partnerships between universities and indigenous communities: A case study in tuatara conservation in Aotearoa

Researchers are increasingly seeking to collaborate cross-culturally, particularly with indig-enous communities. The Kia Mau Te Tītī Mo Ake Tōnu Atu (Keep the Tītī Forever) project is a fantastic example of one such successful effort (Moller et al. 2009). We describe another example of a similarly fruitful relationship between researchers at Victoria University of Wel-lington and Te Atiawa Manawhenua Ki Te Tau Ihu (Te Atiawa)

Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds

BackgroundKiwi represent the most basal extant avian lineage (paleognaths) and exhibit biological attributes that are unusual or extreme among living birds, such as large egg size, strong olfaction, nocturnality, flightlessness and long lifespan. Despite intense interest in their evolution and their threatened status, genomic resources for kiwi were virtually non-existent until the recent publication of a single genome. Here we present the most comprehensive kiwi transcriptomes to date, obtained via Illumina sequencing of whole blood and de novo assembly of mRNA sequences of eight individuals from each of the two rarest kiwi species, little spotted kiwi (LSK; Apteryx owenii) and rowi (A. rowi).ResultsSequences obtained were orthologous with a wide diversity of functional genes despite the sequencing of a single tissue type. Individual and composite assemblies contain more than 7900 unique protein coding transcripts in each of LSK and rowi that show strong homology with chicken (Gallus gallus), including those associated with growth, development, disease resistance, reproduction and behavior. The assemblies also contain 66,909 SNPs that distinguish between LSK and rowi, 12,384 SNPs among LSK (associated with 3088 genes), and 29,313 SNPs among rowi (associated with 4953 genes). We found 3084 transcripts differentially expressed between LSK and rowi and 150 transcripts differentially expressed between the sexes. Of the latter, 83 could be mapped to chicken chromosomes with 95% syntenic with chromosome Z.ConclusionsOur study has simultaneously sequenced multiple species, sexes, and individual kiwi at thousands of genes, and thus represents a significant leap forward in genomic resources available for kiwi. The expression pattern we observed among chromosome Z related genes in kiwi is similar to that observed in ostriches and emu, suggesting a common and ancestral pattern of sex chromosome homomorphy, recombination, and gene dosage among living paleognaths. The transcriptome assemblies described here will provide a rich resource for polymorphic marker development and studies of adaptation of these highly unusual and endangered birds.

Chick Timer™ software proves an accurate disturbance minimising tool for monitoring hatching success in little spotted kiwi (Apteryx owenii)

Measuring hatching success in birds is important for assessing population viability, but nests are often cryptic and may be abandoned if birds are disturbed during nesting. We evaluated the suitability of Wildtech New Zealand Ltds Chick Timer™ radio telemetry software for monitoring hatching success in little spotted kiwi (Apteryx owenii). The software provided accurate reports of activity levels and times of nest emergence by adult birds. Eighty four per cent of incubation attempts and 70% of first hatching events were detected, with no false indications of incubation or hatching. Our results suggest that this technology will facilitate studies of hatching success in little spotted kiwi and other large birds with cryptic or inaccessible nests. A ground truthing study such as this one, however, is required before full implementation of the software in any species.