Genomics detects population structure within and between ocean basins in a circumpolar seabird: The white-chinned petrel

The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (Procellaria aequinoctialis) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and first domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes

Background

The genetic basis of wing development has been well characterised for model insect species, but remains poorly understood in phylogenetically divergent, non-model taxa. Wing-polymorphic insect species potentially provide ideal systems for unravelling the genetic basis of secondary wing reduction. Stoneflies (Plecoptera) represent an anciently derived insect assemblage for which the genetic basis of wing polymorphism remains unclear. We undertake quantitative RNA-seq of sympatric full-winged versus vestigial-winged nymphs of a widespread wing-dimorphic New Zealand stonefly, Zelandoperla fenestrata, to identify genes potentially involved in wing development and secondary wing loss.

Results

Our analysis reveals substantial differential expression of wing-development genes between full-winged versus vestigial-winged stonefly ecotypes. Specifically, of 23 clusters showing significant similarity to Drosophila wing development-related genes and their pea aphid orthologues, nine were significantly upregulated in full-winged stonefly ecotypes, whereas only one cluster (teashirt) was substantially upregulated in the vestigial-winged ecotype.

Conclusions

These findings suggest remarkable conservation of key wing-development pathways throughout 400 Ma of insect evolution. The finding that two Juvenile Hormone pathway clusters were significantly upregulated in vestigial-winged Zelandoperla supports the hypothesis that Juvenile Hormone may play a key role in modulating insect wing polymorphism, as has previously been suggested for other insect lineages.

Genotyping-by-sequencing supports a genetic basis for wing reduction in an alpine New Zealand stonefly

Wing polymorphism is a prominent feature of numerous insect groups, but the genomic basis for this diversity remains poorly understood. Wing reduction is a commonly observed trait in many species of stoneflies, particularly in cold or alpine environments. The widespread New Zealand stonefly Zelandoperla fenestrata species group (Z. fenestrata, Z. tillyardi, Z. pennulata) contains populations ranging from fully winged (macropterous) to vestigial-winged (micropterous), with the latter phenotype typically associated with high altitudes. The presence of flightless forms on numerous mountain ranges, separated by lowland fully winged populations, suggests wing reduction has occurred multiple times. We use Genotyping by Sequencing (GBS) to test for genetic differentiation between fully winged (n = 62) and vestigial-winged (n = 34) individuals, sampled from a sympatric population of distinct wing morphotypes, to test for a genetic basis for wing morphology. While we found no population genetic differentiation between these two morphotypes across 6,843 SNP loci, we did detect several outlier loci that strongly differentiated morphotypes across independent tests. These findings indicate that small regions of the genome are likely to be highly differentiated between morphotypes, suggesting a genetic basis for wing reduction. Our results provide a clear basis for ongoing genomic analysis to elucidate critical regulatory pathways for wing development in Pterygota.

The genomic ancestry, landscape genetics and invasion history of introduced mice in New Zealand

The house mouse (Mus musculus) provides a fascinating system for studying both the genomic basis of reproductive isolation, and the patterns of human-mediated dispersal. New Zealand has a complex history of mouse invasions, and the living descendants of these invaders have genetic ancestry from all three subspecies, although most are primarily descended from M. m. domesticus. We used the GigaMUGA genotyping array (approximately 135 000 loci) to describe the genomic ancestry of 161 mice, sampled from 34 locations from across New Zealand (and one Australian city-Sydney). Of these, two populations, one in the south of the South Island, and one on Chatham Island, showed complete mitochondrial lineage capture, featuring two different lineages of M. m. castaneus mitochondrial DNA but with only M. m. domesticus nuclear ancestry detectable. Mice in the northern and southern parts of the North Island had small traces (approx. 2-3%) of M. m. castaneus nuclear ancestry, and mice in the upper South Island had approximately 7-8% M. m. musculus nuclear ancestry including some Y-chromosomal ancestry-though no detectable M. m. musculus mitochondrial ancestry. This is the most thorough genomic study of introduced populations of house mice yet conducted, and will have relevance to studies of the isolation mechanisms separating subspecies of mice.

Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka)

Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.

An ancient selective sweep linked to reproductive life history evolution in sockeye salmon

Study of parallel (or convergent) phenotypic evolution can provide important insights into processes driving sympatric, ecologically-mediated divergence and speciation, as ecotype pairs may provide a biological replicate of the underlying signals and mechanisms. Here, we provide evidence for a selective sweep creating an island of divergence associated with reproductive behavior in sockeye salmon (Oncorhynchus nerka), identifying a series of linked single nucleotide polymorphisms across a ~22,733 basepair region spanning the leucine-rich repeat-containing protein 9 gene exhibiting signatures of divergent selection associated with stream- and shore-spawning in both anadromous and resident forms across their pan-Pacific distribution. This divergence likely occurred ~3.8 Mya (95% HPD = 2.1–6.03 Mya), after sockeye separated from pink (O. gorbuscha) and chum (O. keta) salmon, but prior to the Pleistocene glaciations. Our results suggest recurrent evolution of reproductive ecotypes across the native range of O. nerka is at least partially associated with divergent selection of pre-existing genetic variation within or linked to this region. As sockeye salmon are unique among Pacific salmonids in their flexibility to spawn in lake-shore benthic environments, this region provides great promise for continued investigation of the genomic basis of O. nerka life history evolution, and, more broadly, for increasing our understanding of the heritable basis of adaptation of complex traits in novel environments.

Sockeye salmon repatriation leads to population re-establishment and rapid introgression with native kokanee

Re‐establishing salmonid populations to areas historically occupied has the substantial potential for conservation gains; however, such interventions also risk negatively impacting native resident stocks. Here, we assessed the success of the hatchery‐assisted reintroduction of anadromous sockeye salmon (Oncorhynchus nerka) into Skaha Lake, British Columbia, Canada, and evaluated the genetic consequences for native kokanee, a freshwater‐obligate ecotype, using single nucleotide polymorphism genotypic data collected from the reference samples of spawning Okanagan River sockeye and Skaha Lake kokanee presockeye reintroduction, along with annual trawl survey and angler‐caught samples obtained over an eight‐year period. Significant differentiation was detected between sockeye and kokanee reference samples, with >99% stock assignment. Low proportions of sockeye and hybrids were detected within 2008 and 2010 age‐0 trawl samples; however, by 2012, 28% were sockeye, rising to 41% in 2014. The number of hybrids detected rose proportionally with the increase in sockeye and exhibited an intermediate phenotype. Our results indicate that the reintroduction of anadromous sockeye to Skaha Lake is succeeding, with large numbers returning to spawn. However, hybridization with native kokanee is of concern due to the potential for demographic or genetic swamping, with ongoing genetic monitoring necessary to assess the long‐term effects of introgression and to support interactive fisheries management.

The complete mitochondrial genomes of two chiton species (Sypharochiton pelliserpentis and Sypharochiton sinclairi) obtained using Illumina next generation sequencing

Using an Illumina platform, we shot-gun sequenced the complete mitochondrial genomes of two sister chiton species (Sypharochiton pelliserpentis and Sypharochiton sinclairi) to an average coverage of 172× and 60×, respectively. We performed a de novo assembly using SOAPdenovo2 and determined the total mitogenome lengths to be 15,048 and 15,028 bps, respectively. The gene organization was similar to that of other chitons, with 13 protein-coding genes, 24 transfer RNAs and 2 ribosomal RNAs. These data will contribute for resolving the taxonomy and population genetic structures of these species.

Providing reviews of evidence to COPD patients: controlled prospective 12-month trial

The aim of this study was to evaluate a novel patient-held manual designed to reduce the evidence–practice gap in chronic obstructive pulmonary disease (COPD). The intervention manual contained summaries of research evidence. It was developed using current best practice for patient information materials and designed to cause discussion of evidence between patient and doctor. A controlled before-and-after study was employed in two similar but geographically separate regions of metropolitan Adelaide, South Australia. Participants had moderate to severe COPD, with 249 included at baseline and 201 completing the study. Evidence-based COPD management was measured using an indicator with three components: rates of influenza vaccination, bone density testing, and pulmonary rehabilitation. A survey of behavioral steps leading to practice change was conducted with the trial. Analysis, by median split of socioeconomic disadvantage, showed significant difference between study arms for only one component of the indicator of evidence-based practice, enrolment in pulmonary rehabilitation and only for the most socioeconomically disadvantaged stratum. For both socioeconomic strata, more intervention participants than control participants reported remembering being given the information material, reading part or all, and finding it very or quite helpful. Other significant differences were restricted to the stratum of greatest socioeconomic disadvantage: reading all of the material, learning from it, referring back, and talking to a doctor about a topic from the material. Above 90% of all participants who received the manual reported reading from it, 42% reported discussing topics with a doctor, but only 10% reported treatment change attributable to the manual. We have found that people with COPD will read an evidence manual developed using current best practice. However, the study demonstrated improvement for only one of the three components of an indicator of evidence-based disease management for only the most socioeconomically disadvantaged stratum of participants. Future interventions should be designed to better translate reading uptake into evidence-based disease management.

Eformoterol n-of-1 trials in chronic obstructive pulmonary disease poorly reversible to salbutamol

AIMS

Benefits of long acting beta 2 agonists are unclear for severe chronic obstructive pulmonary disease (COPD) patients with poor response to short acting bronchodilators. We aimed to evaluate 1) effects of eformoterol in such patients using a 'n-of-1' double crossover study design, and 2) aggregate data as a double-blind, double crossover randomized control trial.

METHODS

Subjects with forced expiratory volume in one second (FEV1) < 60% predicted, and poor response to short acting bronchodilators were studied six times over 18 weeks. During that time they were prescribed four weeks of either eformoterol or placebo, followed by the alternate, and then a second crossover. Four-weekly measures included six minute walk distance (6MWD), FEV1, previous two weeks of symptoms, and chronic respiratory questionnaire (CRQ) including treatment goal items.

RESULTS

Of 27 original subjects (21 male, mean age of 70 years, five smokers, mean prebronchodilator FEV1 36% predicted), one subject had clinically significant concordant improvement in the CRQ dyspnoea domain and 6MWD (by 51 metres), but not for other outcomes. There were no concordant improvements in any other subjects. Aggregate double crossover data analysis demonstrated no improvement in any outcome measures.

CONCLUSIONS

The 'n-of-1' study design and aggregate data analysis demonstrated lack of benefit from eformoterol in COPD patients with poor response to short acting bronchodilators.

'Normal' lung function in rural Australian aborigines

BACKGROUND

Although lung diseases are a leading cause of premature mortality in Australian Aborigines, little is known about normal lung function in these people.

AIM

To develop models for 'normal' spirometric function in rural Australian Aborigines.

METHOD

A cross-sectional population-based study of four rural Aboriginal communities was performed in Queensland, Northern Territory and South Australia, Australia. We studied 261 children aged seven-19 years and 332 adults aged 20-80 years who were free of symptoms and had no clinical signs of chronic lung disease. The outcome measures were forced expiratory volume in one second (FEV1) and forced vital capacity (FVC). Multiple linear regression was used to develop models for FEV1 and FVC and comparisons were made with Caucasians and indigenous people from other countries.

RESULTS

The Aboriginal people studied had FEV1 and FVC values that were lower (20% and 30% respectively) than those found in Caucasians of the same height, age and gender. As a consequence, they had relatively high FEV1/FVC ratios. Those studied also had forced expiratory volumes that were lower than those found in African Americans and other indigenous peoples.

CONCLUSIONS

Apparently healthy rural Aboriginal people have low forced expiratory volumes when contrasted with Caucasians and indigenous peoples such as African Americans. More research is required to determine if this is 'normal' or a product of the suboptimal environment into which many Aboriginal people are born.

Asthma and atopy in four rural Australian aboriginal communities

OBJECTIVE

To determine the prevalence and nature of asthma in four rural Australian Aboriginal communities.

DESIGN

Cross-sectional population study.

SETTING

Four Aboriginal communities in Queensland, the Northern Territory and South Australia, Australia.

SUBJECTS

Data were collected from 1252 subjects aged 5-84 years in August 1990 and August/September 1991.

MAIN OUTCOME MEASURES

Respiratory symptoms, measured by interview-administered questionnaire; airway hyperresponsiveness (AHR), measured by histamine challenge; and allergy, measured by skin-pick tests. AHR was a PD20FEV1 of histamine of less than or equal to 3.9 mumol.

RESULTS

The prevalence of AHR in the four communities ranged from 2.2% to 7.5% and significantly increased with age (chi 2 trend test: P < 0.05). The prevalence of current asthma was 0.5% among 8-12 year old children and 3.3% among adults. The overall prevalence of atopy in the four communities ranged from 21% to 34%. Allergy to cats, house dust mites or cigarette smoking was a risk factor for AHR, and cat allergy was a risk factor for current asthma.

CONCLUSIONS

The prevalence of asthma in rural Aboriginal adults is low in comparison with the prevalence among non-Aboriginal Australians, and asthma in Aboriginal children is almost non-existent. The low prevalence of asthma is possibly due to environmental factors that influence the acquisition of atopy and AHR.