Small domain estimation of census coverage: A case study in Bayesian analysis of complex survey data

Many countries conduct a full census survey to report official population statistics. As no census survey ever achieves 100 per cent response rate, a post-enumeration survey (PES) is usually conducted and analysed to assess census coverage and produce official population estimates by geographic area and demographic attributes. Considering the usually small size of PES, direct estimation at the desired level of disaggregation is not feasible. Design-based estimation with sampling weight adjustment is a commonly used method but is difficult to implement when survey non-response patterns cannot be fully documented and population benchmarks are not available. We overcome these limitations with a fully model-based Bayesian approach applied to the New Zealand PES. Although theory for the Bayesian treatment of complex surveys has been described, published applications of individual level Bayesian models for complex survey data remain scarce. We provide such an application through a case study of the 2018 census and PES surveys. We implement a multilevel model that accounts for the complex design of PES. We then illustrate how mixed posterior predictive checking and cross-validation can assist with model building and model selection. Finally, we discuss potential methodological improvements to the model and potential solutions to mitigate dependence between the two surveys.Comment: 35 pages, 5 figures This is an author version of a paper accepted for publication in the Journal of Official Statistics. Once published by the Journal of Official Statistics use the Journal citation. This version includes supplementary material and corrected version of Figure

Selection and gene flow shape genomic islands that control floral guides

Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding "sea," making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation

Linking demographic history and evolution at the expanding range edge of Sitka spruce (Picea sitchensis)

Anthropogenic climate change is shifting species ranges and exerting high selection pressures on populations of all taxa, including trees. Temperate tree species of the northern hemisphere share a history of large-scale postglacial colonization during the Quaternary, providing a natural laboratory for the study of evolutionary responses to climate fluctuations. This dissertation aims at improving our understanding of the mutual influences of demography and evolutionary patterns during range expansions in trees using Picea sitchensis (Sitka spruce) as a focal species. I first focused on the most recent P. sitchensis expansion event in south-central Alaska to study the interplay between demography and population genetics by combining neutral genetic markers and tree ring data. This multidisciplinary approach allowed me to assess the pace of neutral evolution across five centuries of colonization. Allelic richness was efficiently recovered in the colonizing population by early, open-grown colonizers on the Kodiak Archipelago during a long phase of low population growth. However, heterozygosity remains low compared with the nearest mainland populations. These results highlight the long-term importance of early colonizing genotypes in genetics of populations and the influence of pollen dispersal in maintaining standing genetic variation during forest expansion. Local hybridization of P. sitchensis colonizers with foreign pollen from white spruce (Picea glauca) populations occurred repeatedly during the early colonization period. However, introgression was suppressed in subsequent generations growing under a closed canopy. As the two species occupy separate climatic niches, selection against hybrids, intensified by competition, might explain this pattern. Spring precipitation tended to affect hybrid growth more negatively than pure P. sitchensis genotypes, but this effect was nonsignificant. I finally assessed the extent to which demographic parameters of range expansion can be estimated from genomic data through simulations using the approximate Bayesian computation framework. Simple 3-parameter models could be successfully estimated with genetic markers developed from reduced-representation methods currently available for nonmodel species. Models of higher complexity presented challenges, especially when ongoing migration after expansion was considered, and the accuracy of results depended on the time of expansion. The demic expansion models examined here were inadequate to infer the colonization history of P. sitchensis.Forestry, Faculty ofGraduat