Population genomics of the critically endangered kākāpō

Summary The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species

Data from: Evidence for Bergmann's rule and not allopatric subspeciation in the threatened kaka (Nestor meridionalis)

Species of conservation concern characterized by small and declining populations greatly benefit from proactive management approaches such as population translocations. Because they often show intra-specific genetic and phenotypic variation, which can result from drift or differential selective pressures between habitats, understanding the distribution of such variation and its underlying processes is a prerequisite to develop effective management guidelines. Indeed, translocations among genetically differentiated populations potentially locally adapted are discouraged in order to avoid outbreeding depression, while translocations among populations characterized by high gene flow with no evidence for local adaptation are encouraged. Here, we first test whether 2 recognized subspecies, the North Island kaka (Nestor meridionalis septentrionalis) and South Island kaka (Nestor meridionalis meridionalis) of New Zealand fit a scenario of allopatric subspeciation following the separation of the North and South Islands at the end of the Pleistocene using 1 mtDNA (n = 96) and 9 microsatellite markers (n = 126). We then test whether morphological differences among the 2 subspecies support a pattern of local adaptation, comparing phenotypic divergence (P ST) and the level of divergence by drift alone (F ST) among populations. We find little population structure between islands, ruling out allopatric subspeciation in kaka. Further, P ST exceeds F ST, supporting an adaptive latitudinal size cline consistent with Bergmann’s rule. These results therefore suggest that using neutral genetic diversity alone can be misleading when identifying management units and that the nature of phenotypic variation should be considered in translocations efforts. We finally discuss North and South Island management units but suggest that cross-island translocation be allowed

Kaka_population_coordinates

Nestor meridonalis samplig locations names and coordinate

kaka morphometrics

Nestor meridonalis morphometrics with bill length, weight, tarsus length, wing length measured on 627 bird

Kaka_msat_genotypes

Nestor meridionalis microsatellite genotypes for 9 loci and 126 sample

Kaka_mtDNA_CR

Nestor meridonalis mitocondrial Control region sequences (940 bp) for 96 sample

Paper 11 NEW.indd

Abstract The reproduction of kakapo (Strigops habroptilus) on offshore island refuges was monitored between 1990 and 2002. Productivity was primarily determined by the proportion of females that nested each breeding year. Within the same island, the proportion of females nesting each breeding year ranged between 33 -95% but, as a proportion of the total female population, was just 5 -42% between 1990 and 1999. The deliberate placement of the entire adult female population on Codfi sh Island (Whenua Hou) in anticipation of an exceptional fruit crop resulted in 95% of them nesting in 2002, raising 24 fl edglings and increasing the total population by 39%. Although efforts to increase the frequency of kakapo breeding by providing supplementary food have been unsuccessful, nesting and fl edging success increased signifi cantly following the introduction of new, more intensive, management methods in 1995. Hatching success has, however, remained poor, with just 42% of eggs hatching. Comparison with related parrot species suggests that the kakapo's hatching success is unusually low, perhaps because of inbreeding. Despite infrequent breeding and poor hatching success, the kakapo population has increased by 69% from 51 birds i

Micronutrient Deficiency and Treatment Adherence in a Randomized Controlled Trial of Micronutrient Supplementation in ART-Naïve Persons with HIV

<div><p>Introduction</p><p>The MAINTAIN study is an on-going RCT comparing high-dose micronutrient and anti-oxidant supplementation versus recommended daily allowance (RDA) vitamins in slowing HIV immune deficiency progression in ART-naïve people with HIV infection.</p><p>Objective</p><p>We planned analysis of the first 127 participants to determine the baseline prevalence of serum micronutrient deficiencies and correlates, as well as tolerance and adherence to study interventions.</p><p>Methods</p><p>Participants receive eight capsules twice daily of 1) high-dose or 2) RDA supplements for two years and are followed-up quarterly for measures of immune deficiency progression, safety and tolerability. Regression analysis was used to identify correlates of micronutrient levels at baseline. Adherence was measured by residual pill count, self-report using the General Treatment Scale (GTS) and short-term recall HIV Adherence Treatment Scale (HATS).</p><p>Results</p><p>Prior micronutrient supplementation (within 30 days) was 27% at screening and 10% of study population, and was not correlated with baseline micronutrient levels. Low levels were frequent for carotene (24%<1 nmol/L), vitamin D (24%<40 nmol/L) and serum folate (20%<15 nmol/L). The proportion with B₁₂ deficiency (<133 pmol/L) was 2.4%. Lower baseline levels of B₁₂ correlated lower baseline CD4 count (r = 0.21, p = 0.02) with a 21 pmol/L reduction in B₁₂ per 100 cells/µL CD4. Vitamin D levels were higher in men (p<0.001). After a median follow-up of 1.63 years, there were 19 (15%) early withdrawals from the study treatment. Mean treatment adherence using pill count was 88%. Subjective adherence by the GTS was 81% and was moderately but significantly correlated with pill count (r = 0.29, p<0.001). Adherence based on short-term recall (HATS) was >80% in 75% of participants.</p><p>Conclusion</p><p>Micronutrient levels in asymptomatic HIV+ persons are in keeping with population norms, but micronutrient deficiencies are frequent. Adherence levels are high, and will permit a valid evaluation of treatment effects.</p><p>Trial Registration</p><p>ClinicalTrials.gov <a href="http://clinicaltrials.gov/show/NCT00798772" target="_blank">NCT00798772</a></p></div

Treatment adherence by residual pill count over time.

<p>The data points and bars indicate mean percentage and standard deviation of the expected unreturned medication capsules on the Y-axis. The X-axis indicates the study follow-up visit week. The number of subjects included in analysis is included under the X-axis. Imputation of average adherence was used for missing values.</p

Average treatment adherence by returned capsule count, and with multiple imputation for non-returns.

<p>Adherence to study medication over time was assessed by counting capsule packets returned at weeks 12, 24, 36, 48, 60, 72 and 84. Treatment adherence was calculated and compared using different methods. When only those who attended visits and returned capsule packets were included in analysis, average adherence was 88%. Intention-to-treat analysis, with 26% imputation for missing returns, yielded three estimates: 66% (0% imputed for missing values), 91% (100% imputed for missing values), and 88% (average adherence of returns imputed for missing values).</p