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Register a new userGenomic tests of variation in inbreeding among individuals and among chromosomes
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We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about inbreeding when a relatively small set of whole-genome sequences is available. Rather than focus on testing for deviations from Hardy-Weinberg genotype frequencies at each site, we analyze the entire distribution of heterozygotes conditioned on the number of copies of the derived (non-chimpanzee) allele. Using Levenes exact test, we reject Hardy-Weinberg in both populations. We generalized Levenes distribution to obtain the exact distribution of the number of heterozygous individuals given that every individual has the same inbreeding coefficient, F. We estimated F to be 0.0026 in Europeans and 0.0005 in Yorubans, but we could also reject the hypothesis that F was the same in each individual. We used a composite likelihood method to estimate F in each individual and within each chromosome. Variation in F across chromosomes within individuals was too large to be consistent with sampling effects alone. Furthermore, estimates of F for each chromosome in different populations were not correlated. Our results show how detailed comparisons of population genomic data can be made to theoretical predictions. The application of methods to the Complete Genomics data set shows that the extent of apparent inbreeding varies across chromosomes and across individuals, and estimates of inbreeding coefficients are subject to unexpected levels of variation which might be partly accounted for by selection.
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Generally, genotypes and phenotypes are expected to be spatially congruent, however, in widespread species complexes with few barriers to dispersal, multiple contact zones, and limited reproductive isolation, discordance between phenotypes and phylogeographic groups is more probable. Wagtails (Aves: Motacilla) are a genus of birds with striking plumage pattern variation across Eurasia. Up to 13 subspecies are recognized within a single species, yet previous studies using mitochondrial DNA have supported phylogeographic groups that are inconsistent with subspecies plumage characteristics. In this study, we investigate the link between phenotypes and genotype by comparing populations thought to be at different stages along the speciation continuum. We take a phylogeographic approach by estimating population structure, testing for isolation by distance, conducting demographic modeling, and estimating the first time-calibrated species tree for the genus. Our study provides strong evidence for species-level patterns of differentiation in wagtails, however population-level differentiation is less pronounced. We find evidence that three of four widespread Eurasian species exhibit an east-west divide that contradicts both subspecies taxonomy and phenotypic variation. Both the geographic location of this divide and time estimates from demographic models are overlapping in two sympatric species, indicating that coincident Pleistocene events shaped their histories.
Improved monitoring and associated inferential tools to efficiently identify declining bird populations, particularly of rare or sparsely distributed species, is key to informed conservation and management across large spatio-temporal regions. We assess abundance trends for 106 bird species in a network of eight national park forests located within the northeast USA from 2006-2019 using a novel hierarchical model. We develop a multi-species, multi-region removal sampling model that shares information across species and parks to enable inference on rare species and sparsely sampled parks and to evaluate the effects of local forest structure. Trends in bird abundance over time varied widely across parks, but species showed similar trends within parks. Three parks (Acadia, Marsh-Billings-Rockefeller, and Morristown) decreased in bird abundance across all species, while three parks (Saratoga, Roosevelt-Vanderbilt, and Weir-Farm) increased in abundance. Bird abundance peaked at medium levels of basal area and high levels of percent forest and forest regeneration, with percent forest having the largest effect. Variation in these effects across parks could be a result of differences in forest structural stage and diversity. Our novel hierarchical model enables estimates of abundance at the network, park, guild, and species levels. We found large variation in abundance trends across parks but not across bird guilds, suggesting that local forest condition may have a broad and consistent effect on the entire bird community within a given park. Management should target the three parks with overall decreasing trends in bird abundance to further identify what specific factors are driving observed declines across the bird community. Understanding how bird communities respond to local forest structure and other stressors is crucial for informed and lasting management.
Understanding systems level behaviour of many interacting agents is challenging in various ways, here well focus on the how the interaction between components can lead to hierarchical structures with different types of dynamics, or causations, at different levels. We use the Tangled Nature model to discuss the co-evolutionary aspects connecting the microscopic level of the individual to the macroscopic systems level. At the microscopic level the individual agent may undergo evolutionary changes due to mutations of strategies. The micro-dynamics always run at a constant rate. Nevertheless, the systems level dynamics exhibit a completely different type of intermittent abrupt dynamics where major upheavals keep throwing the system between meta-stable configurations. These dramatic transitions are described by a log-Poisson time statistics. The long time effect is a collectively adapted of the ecological network. We discuss the ecological and macroevolutionary consequences of the adaptive dynamics and briefly describe work using the Tangled Nature framework to analyse problems in economics, sociology, innovation and sustainability
The population in the sexual Penna ageing model is first separated into several reproductively isolated groups. Then, after equilibration, sexual mixing between the groups is allowed. We study the changes in the population size due to this mixing and interpret them through a counterplay of purifying selection and of haplotype complementarity.
Objective: To conduct a meta-analysis of current studies that examined sex differences in severity and mortality in patients with COVID-19, and identify potential mechanisms underpinning these differences. Methods: We performed a systematic review to collate data from observational studies examining associations of sex differences with clinical outcomes of COVID-19. PubMed, Web of Science and four preprint servers were searched for relevant studies. Data were extracted and analyzed using meta-analysis where possible, with summary data presented otherwise. Publicly available bulk RNA sequencing (RNA-seq), single-cell RNA sequencing (scRNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) data were analyzed to explore the potential mechanisms underlying the observed association. Results: 39 studies met inclusion criteria, representing 77932 patients, of which 41510 (53.3%) were males. Men were at a markedly increased risk of developing severe cases compared with women. Furthermore, the pooled odds ratio (OR) of mortality for male group compared with the female group indicated significant higher mortality rate for male. Data from scRNA-seq suggest that men have a higher amount of ACE2-expressing pulmonary alveolar type II cells than women. Sex-based immunological differences exist. The expression of androgen receptor (AR) is positively correlated with ACE2, and there is evidence that AR may directly regulate the expression of ACE2. Conclusions: This meta-analysis detected an increased severity and mortality rate in the male populations with COVID-19, which might be attributable to the sex-based differences in cellular compositions and immunological microenvironments of the lung. The host cell receptor ACE2 is likely regulated by AR signaling pathway, which is identified as a potential target for prevention and treatment of SARS-Cov-2 infections in men.
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