Assessing the Accuracy and Power of Population Genetic Inference from Low-Pass Next-Generation Sequencing Data

Next-generation sequencing (NGS) technologies have made it possible to address population genetic questions in almost any system, but high error rates associated with such data can introduce significant biases into downstream analyses, necessitating careful experimental design and interpretation in studies based on short-read sequencing. Exploration of population genetic analyses based on NGS has revealed some of the potential biases, but previous work has emphasized parameters relevant to human population genetics and further examination of parameters relevant to other systems is necessary, including situations where sample sizes are small and genetic variation is high. To assess experimental power to address several principal objectives of population genetic studies under these conditions, we simulated population samples under selective sweep, population growth, and population subdivision models and tested the power to accurately infer population genetic parameters from sequence polymorphism data obtained through simulated 4×, 8×, and 15× read depth sequence data. We found that estimates of population genetic differentiation and population growth parameters were systematically biased when inference was based on 4× sequencing, but biases were markedly reduced at even 8× read depth. We also found that the power to identify footprints of positive selection depends on an interaction between read depth and the strength of selection, with strong selection being recovered consistently at all read depths, but weak selection requiring deeper read depths for reliable detection. Although we have explored only a small subset of the many possible experimental designs and population genetic models, using only one SNP-calling approach, our results reveal some general patterns and provide some assessment of what biases could be expected under similar experimental structures

Tribal vs. Public Schools: Perceived Discrimination and School Adjustment among Indigenous Children from Early to Mid- Adolescence

The purpose of this study is to assess the differential effects of perceived discrimination by type of school on positive school adjustment among Indigenous children during late elementary and early middle school years. The analysis utilizes a sample of 654 Indigenous children from four reservations in the Northern Midwest and four Canadian First Nation reserves. Multiple group linear growth modeling within a structural equation framework is employed to investigate the moderating effects of school type on the relationship between discrimination and positive school adjustment. Results show that students in all school types score relatively high on positive school adjustment at time one (ages 10-12). However, in contrast to students in tribal schools for whom positive school adjustment remains stable, those attending public schools and those moving between school types show a decline in school adjustment over time. Furthermore, the negative effects of discrimination on positive school adjustment are greater for those attending public schools and those moving between schools. Possible reasons for this finding and potential explanations for why tribal schools may provide protection from the negative effects of discrimination are discussed

Tribal vs. Public Schools: Perceived Discrimination and School Adjustment among Indigenous Children from Early to Mid- Adolescence

The purpose of this study is to assess the differential effects of perceived discrimination by type of school on positive school adjustment among Indigenous children during late elementary and early middle school years. The analysis utilizes a sample of 654 Indigenous children from four reservations in the Northern Midwest and four Canadian First Nation reserves. Multiple group linear growth modeling within a structural equation framework is employed to investigate the moderating effects of school type on the relationship between discrimination and positive school adjustment. Results show that students in all school types score relatively high on positive school adjustment at time one (ages 10-12). However, in contrast to students in tribal schools for whom positive school adjustment remains stable, those attending public schools and those moving between school types show a decline in school adjustment over time. Furthermore, the negative effects of discrimination on positive school adjustment are greater for those attending public schools and those moving between schools. Possible reasons for this finding and potential explanations for why tribal schools may provide protection from the negative effects of discrimination are discussed

Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth

One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 US Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of over 13 000 loci to infer the demographic history of pupfishes in Death Valley. Instead of relicts isolated 2–3 Myr ago throughout repeated flooding of the entire region by inland seas as currently believed, we present evidence for frequent gene flow among Death Valley pupfish species and divergence after the most recent flooding 13 kyr ago. We estimate that Devils Hole was colonized by pupfish between 105 and 830 years ago, followed by genetic assimilation of pelvic fin loss and recent gene flow into neighbouring spring systems. Our results provide a new perspective on an iconic endangered species using the latest population genomic methods and support an emerging consensus that timescales for speciation are overestimated in many groups of rapidly evolving species

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 435 wild rice accessions. We show that most modern wild rice is heavily admixed with domesticated rice through both pollen- and seed-mediated gene flow. In fact, much presumed wild rice may simply represent different stages of feralized domesticated rice. In line with this hypothesis, many presumed wild rice varieties show remnants of the effects of selective sweeps in previously identified domestication genes, as well as evidence of recent selection in flowering genes possibly associated with the feralization process. Furthermore, there is a distinct geographical pattern of gene flow from aus, indica, and japonica varieties into colocated wild rice. We also show that admixture from aus and indica is more recent than gene flow from japonica, possibly consistent with an earlier spread of japonica varieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow

Evidence for divergent selection between the molecular forms of Anopheles gambiae: role of predation

The molecular forms of Anopheles gambiae are undergoing speciation. They are characterized by a strong assortative mating and they display partial habitat segregation. The M form is mostly found in flooded/irrigated areas whereas the S form dominates in the surrounding areas, but the ecological factors that shape this habitat segregation are not known. Resource competition has been demonstrated between species undergoing divergent selection, but resource competition is not the only factor that can lead to divergence. In a field experiment using transplantation of first instar larvae, we evaluated the role of larval predators in mediating habitat segregation between the forms. We found a significant difference in the ability of the molecular forms to exploit the different larval sites conditioned on the presence of predators. In absence of predation, the molecular forms outcompeted each other in their respective natural habitats however, the developmental success of the M form was significantly higher than that of the S form in both habitats under predator pressure. Our results provide the first empirical evidence for specific adaptive differences between the molecular forms and stress the role of larval predation as one of the mechanisms contributing to their divergence.https://doi.org/10.1186/1471-2148-8-

Analysis of the atmospheric distribution, sources, and sinks of oxygenated volatile organic chemicals based on measurements over the Pacific during TRACE-P

Airborne measurements of a large number of oxygenated volatile organic chemicals (OVOC) were carried out in the Pacific troposphere (0.1 - 12 km) in winter/spring of 2001 (24 February to 10 April). Specifically, these measurements included acetone (CH3COCHA3), methylethyl ketone (CH3COC2H5, MEK), methanol (CH3OH), ethanol (C2H5OH), acetaldehyde (CH3CHO), propionaldehyde C2H 5CHO), peroxyacylnitrates (PANs) (CnH 2n+1COO2NO2), and organic nitrates (CnH2n+1ONO2). Complementary measurements of formaldehyde (HCHO), methyl hydroperoxide (CH 3OOH), and selected tracers were also available. OVOC were abundant in the clean troposphere and were greatly enhanced in the outflow regions from Asia. Background mixing ratios were typically highest in the lower troposphere and declined toward the upper troposphere and the lowermost stratosphere. Their total abundance (ΣOVOC) was nearly twice that of nonmethane hydrocarbons (Σ C2-C8 NMHC. Throughout the troposphere, the OH reactivity of OVOC is comparable to that of methane and far exceeds that of NMHC. A comparison of these data with western Pacific observations collected some 7 years earlier (February-March 1994) did not reveal significant differences. Mixing ratios of OVOC were strongly correlated with each other as well as with tracers of fossil and biomass/biofuel combustion. Analysis of the relative enhancement of selected OVOC with respect to CH 3Cl and CO in 12 plumes originating from fires and sampled in the free troposphere (3-11 km) is used to assess their primary and secondary emissions from biomass combustion. The composition of these plumes also indicates a large shift of reactive nitrogen into the PAN reservoir thereby limiting ozone formation. A three-dimensional global model that uses state of the art chemistry and source information is used to compare measured and simulated mixing ratios of selected OVOC. While there is reasonable agreement in many cases, measured aldehyde concentrations are significantly larger than predicted. At their observed levels, acetaldehyde mixing ratios are shown to be an important source of HCHO (and HOx) and PAN in the troposphere. On the basis of presently known chemistry, measured mixing ratios of aldehydes and PANs are mutually incompatible. We provide rough estimates of the global sources of several OVOC and conclude that collectively these are extremely large (150-500 Tg C yr-1) but remain poorly quantified. Copyright 2004 by the American Geophysical Union

Effect of BG-Lures on the Male Aedes (Diptera: Culicidae) Sound Trap capture rates

With global expansion of the two main vectors of dengue, Aedes aegypti (Linnaeus, Diptera: Culicidae) and Aedes albopictus (Skuse, Diptera: Culicidae), there is a need to further develop cost-effective and user-friendly surveillance tools to monitor the population dynamics of these species. The abundance of Ae. aegypti and Ae. Albopictus, and associated bycatch captured by Male Aedes Sound Traps (MASTs) and BG-Sentinel (BGS) traps that were unbaited or baited with BG-Lures were compared in Cairns, Australia and Madang, Papua New Guinea. Mean male Ae. aegypti and Ae. albopictus catch rates in MASTs did not significantly differ when deployed with BG-Lures. Similarly, males of both these species were not sampled at statistically different rates in BGS traps with or without BG-Lures. However, MASTs with BG-Lures caught significantly less male Ae. aegypti than BGS traps baited with BG-Lures in Cairns, and MASTs without BG-Lures caught significantly more male Ae. albopictus than BGS traps without BG-Lures in Madang. Additionally, BG-Lures significantly increased female Ae. aegypti catch rates in BGS traps in Cairns. Lastly, bycatch capture rates in BGS traps were not significantly influenced by the addition of the BG-Lures. While this study provides useful information regarding the surveillance of Ae. aegypti and Ae. albopictus in these locations, further development and investigation is required to successfully integrate an olfactory lure into the MAST system

The potential role of hybridization in diversification and speciation in an insular plant lineage: insights from synthetic interspecific hybrids

Hybridization is recognized as an important process in plant evolution, and this may be particularly true for island plants where several biotic and abiotic factors facilitate interspecific hybridization. Although rarely done, experimental studies could provide insights into the potential of natural hybridization to generate diversity when species come into contact in the dynamic island setting. The potential of hybridization to generate morphological variation was analysed within and among 12 families (inbred lines) of an F4 hybrid generation between two species of Tolpis endemic to the Canary Islands. Combinations of characters not seen in the parents were present in hybrids. Several floral and vegetative characters were transgressive relative to their parents. Morphometric studies of floral, vegetative and fruit characters revealed that several F4 families were phenotypically distinct from other families, and from their parents. The study demonstrates that morphologically distinct pollen-fertile lines, potentially worthy of taxonomic recognition if occurring in nature, can be generated in four generations. The ability of the hybrid lines to set self-seed would reduce gene flow among the lines, and among the hybrids and their parental species. Selfing would also facilitate the fixation of characters within each of the lines. Overall, the results show the considerable potential of hybridization for generating diversity and distinct phenotypes in island lineages

Environmental influences on Aedes aegypti catches in Biogents Sentinel traps during a Californian "rear and release" program: implications for designing surveillance programs

As Aedes aegypti continues to expand its global distribution, the diseases it vectors (dengue, Zika, chikungunya and yellow fever) are of increasing concern. Modern efforts to control this species include "rear and release" strategies where lab-reared mosquitoes are distributed throughout the landscape to replace or suppress invasive populations. These programs require intensive surveillance efforts to monitor their success, and the Biogents Sentinel (BGS) trap is one of the most effective tools for sampling adult Ae. aegypti. BGS trap catches can be highly variable throughout landscapes, so we investigated the potential impacts of environmental factors on adult Ae. aegypti capture rates during a "rear and release" program in California to better understand the relative contributions of true variability in population density across a landscape and trap context. We recorded male and female Ae. aegypti catches from BGS traps, with and without CO2, throughout control sites where no mosquitoes were released and in treatment sites where males infected with Wolbachia were released. BGS trap catches were positively influenced by higher proportions of shade or bushes in the front yard of the premises as well as the presence of potential larval habitats such as subterranean vaults. In contrast, an increase in residential habitat within a 100 m radius of trap locations negatively influenced BGS trap catches. For male Ae. aegypti, increased visual complexity of the trap location positively influenced capture rates, and the presence of yard drains negatively affected catch rates in control sites. Lastly, for BGS traps using CO2, higher catch rates were noted from traps placed greater than one meter from walls or fences for both male and female mosquitoes. These results have important implications for surveillance programs of Ae. aegypti throughout the Californian urban environment including adult monitoring during "rear and release" programs