The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean.

Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that barn owls colonized the Western Palearctic in a ring-like manner around the Mediterranean and meet in secondary contact in Greece. Rufous coloration appears to be linked to a recently evolved nonsynonymous-derived variant of the melanocortin 1 receptor (MC1R) gene, which according to quantitative genetic analyses evolved under local adaptation during or following the colonization of Central Europe. Admixture patterns and linkage disequilibrium between the neutral genetic background and color found exclusively within the secondary contact zone suggest limited introgression at secondary contact. These results from a system reminiscent of ring species provide a striking example of how local adaptation can evolve from derived genetic variation

The geographic mosaic of herbicide resistance evolution in the common morning glory, Ipomoea purpurea: Evidence for resistance hotspots and low genetic differentiation across the landscape

Strong human‐mediated selection via herbicide application in agroecosystems has repeatedly led to the evolution of resistance in weedy plants. Although resistance can occur among separate populations of a species across the landscape, the spatial scale of resistance in many weeds is often left unexamined. We assessed the potential that resistance to the herbicide glyphosate in the agricultural weed Ipomoea purpurea has evolved independently multiple times across its North American range. We examined both adaptive and neutral genetic variations in 44 populations of I. purpurea by pairing a replicated dose–response greenhouse experiment with SSR genotyping of experimental individuals. We uncovered a mosaic pattern of resistance across the landscape, with some populations exhibiting high‐survival postherbicide and other populations showing high death. SSR genotyping revealed little evidence of isolation by distance and very little neutral genetic structure associated with geography. An approximate Bayesian computation (ABC) analysis uncovered evidence for migration and admixture among populations before the widespread use of glyphosate rather than the very recent contemporary gene flow. The pattern of adaptive and neutral genetic variations indicates that resistance in this mixed‐mating weed species appears to have evolved in independent hotspots rather than through transmission of resistance alleles across the landscape.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113156/1/eva12290_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/113156/2/eva12290.pd

Unhealthy food and beverage consumption during childhood and risk of cardiometabolic disease: a systematic review of prospective cohort studies

Background Global consumption of unhealthy foods, including ultra-processed foods (UPFs) and sugar-sweetened beverages (SSBs), has increased substantially among pediatric populations. Suboptimal diet during early life can track into adulthood, alongside risk factors for cardiometabolic disease. Objective To inform the development of updated WHO guiding principles for complementary feeding of infants and young children, this systematic review sought to examine the association between unhealthy food consumption during childhood and cardiometabolic risk biomarkers. Methods PubMed (Medline), EMBASE, and Cochrane CENTRAL were systematically searched, with no language restriction, up to 10 March 2022. Inclusion criteria were randomized controlled trials (RCTs), non-RCTs, and longitudinal cohort studies; children aged ≤10.9 y at exposure; studies reporting greater consumption of unhealthy foods and beverages (defined using nutrient- and food-based approaches) than no or low consumption; studies assessing critical nonanthropometric cardiometabolic disease risk outcomes (blood lipid profile, glycemic control, or blood pressure). Results Of 30,021 identified citations, 11 articles from 8 longitudinal cohort studies were included. Six studies focused on exposure to unhealthy foods or UPF, and 4 focused on SSB only. Methodological heterogeneity was too high across studies to meta-analyze effect estimates. A narrative synthesis of quantitative data revealed that exposure to unhealthy foods and beverages, specifically NOVA-defined UPF, in children of preschool age may be associated with a worse blood lipid and blood pressure profile in later childhood (Grading of Recommendations Assessment, Development, and Evaluation [GRADE]: low and very low certainty, respectively). No associations were evident between SSB consumption and blood lipids, glycemic control, or blood pressure (GRADE: all low certainty). Conclusions No definitive conclusion can be made because of quality of the data. More high-quality studies that purposefully assess the effects of unhealthy food and beverage exposure during childhood on cardiometabolic risk outcomes are needed. This protocol was registered at https://www.crd.york.ac.uk/PROSPERO/ as CRD42020218109

Unhealthy food and beverage consumption in children and risk of overweight and obesity: a systematic review and meta-analysis

This WHO-commissioned review contributed to the update of complementary feeding recommendations, synthesizing evidence on effects of unhealthy food and beverage consumption in children on overweight and obesity. We searched PubMed (Medline), Cochrane CENTRAL and Embase for articles, irrespective of language or geography. Inclusion criteria were: 1) randomized controlled trials (RCTs); non-RCTs; cohort studies and pre/post studies with control; 2) participants ≤ 10.9 y at exposure; 3) studies reporting greater consumption of unhealthy foods/beverages vs. no or low consumption; 4) studies assessing anthropometric and/or body composition; and 5) publication date ≥ 1971. Unhealthy foods and beverages were defined using nutrient- and food-based approaches. Risk of bias was assessed using the ROBINS-I and RoB2 tools for non-randomized and randomized studies, respectively. Narrative synthesis was complemented by meta-analyses where appropriate. Certainty of evidence was assessed using GRADE. Of 26,542 identified citations, 60 studies from 71 articles were included. Most studies were observational (59/60), and no included studies were from low-income countries. The evidence base was low quality, as assessed by ROBINS-I and RoB2 tools. Evidence synthesis was limited by the different interventions and comparators across studies. Evidence indicated that consumption of sugar-sweetened beverages (SSB) and unhealthy foods in childhood may increase body mass index (BMI)/BMI z-score, % body fat or odds of overweight/obesity (low certainty of evidence). Artificially-sweetened beverages and 100% fruit juice consumption may make little/no difference to BMI, % body fat or overweight/obesity outcomes (low certainty of evidence). Meta-analyses of a subset of studies indicated a positive association between SSB intake and % body fat, but no association with change in BMI and BMI z-score. High-quality epidemiological studies that are designed to assess the effects of unhealthy food consumption during childhood on risk of overweight/obesity are needed to contribute to a more robust evidence base upon which to design policy recommendations. This protocol was registered at https://www.crd.york.ac.uk/PROSPERO as CRD42020218109

Evolutionary aspects of population structure for molecular and quantitative traits in the freshwater snail Radix balthica.

Detecting the action of selection in natural populations can be achieved using the QST-FST comparison that relies on the estimation of FST with neutral markers, and QST using quantitative traits potentially under selection. QST higher than FST suggests the action of directional selection and thus potential local adaptation. In this article, we apply the QST-FST comparison to four populations of the hermaphroditic freshwater snail Radix balthica located in a floodplain habitat. In contrast to most studies published so far, we did not detect evidence of directional selection for local optima for any of the traits we measured: QST calculated using three different methods was never higher than FST. A strong inbreeding depression was also detected, indicating that outcrossing is probably predominant over selfing in the studied populations. Our results suggest that in this floodplain habitat, local adaptation of R. balthica populations may be hindered by genetic drift, and possibly altered by uneven gene flow linked to flood frequency

Differential Dynamics of Transposable Elements during Long-Term Diploidization of Nicotiana Section Repandae (Solanaceae) Allopolyploid Genomes

PubMed ID: 23185607This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Comparative population structure of <i>Plasmodium malariae</i> and <i>Plasmodium falciparum</i> under different transmission settings in Malawi

&lt;b&gt;Background:&lt;/b&gt; Described here is the first population genetic study of Plasmodium malariae, the causative agent of quartan malaria. Although not as deadly as Plasmodium falciparum, P. malariae is more common than previously thought, and is frequently in sympatry and co-infection with P. falciparum, making its study increasingly important. This study compares the population parameters of the two species in two districts of Malawi with different malaria transmission patterns - one seasonal, one perennial - to explore the effects of transmission on population structures. &lt;BR/&gt; &lt;b&gt;Methods:&lt;/b&gt; Six species-specific microsatellite markers were used to analyse 257 P. malariae samples and 257 P. falciparum samples matched for age, gender and village of residence. Allele sizes were scored to within 2 bp for each locus and haplotypes were constructed from dominant alleles in multiple infections. Analysis of multiplicity of infection (MOI), population differentiation, clustering of haplotypes and linkage disequilibrium was performed for both species. Regression analyses were used to determine association of MOI measurements with clinical malaria parameters. &lt;BR/&gt; &lt;b&gt;Results:&lt;/b&gt; Multiple-genotype infections within each species were common in both districts, accounting for 86.0% of P. falciparum and 73.2% of P. malariae infections and did not differ significantly with transmission setting. Mean MOI of P. falciparum was increased under perennial transmission compared with seasonal (3.14 vs 2.59, p = 0.008) and was greater in children compared with adults. In contrast, P. malariae mean MOI was similar between transmission settings (2.12 vs 2.11) and there was no difference between children and adults. Population differentiation showed no significant differences between villages or districts for either species. There was no evidence of geographical clustering of haplotypes. Linkage disequilibrium amongst loci was found only for P. falciparum samples from the seasonal transmission setting. &lt;BR/&gt; &lt;b&gt;Conclusions:&lt;/b&gt; The extent of similarity between P. falciparum and P. malariae population structure described by the high level of multiple infection, the lack of significant population differentiation or haplotype clustering and lack of linkage disequilibrium is surprising given the differences in the biological features of these species that suggest a reduced potential for out-crossing and transmission in P. malariae. The absence of a rise in P. malariae MOI with increased transmission or a reduction in MOI with age could be explained by differences in the duration of infection or degree of immunity compared to P. falciparum

The Population Structure of Glossina palpalis gambiensis from Island and Continental Locations in Coastal Guinea

Guinea is the country with the highest prevalence of sleeping sickness in West Africa, and we undertook a population genetics analysis there of the most dangerous tsetse fly species of West Africa, Glossina palpalis gambiensis. Our aims were to estimate effective population size and the degree of isolation between coastal sites on the mainland of Guinea (including Dubréka, a highly prevalent sleeping sickness focus) and Loos Islands in order to get the most possible accurate vision of feasibility and sustainability of anti-tsetse strategies of these sites. We found very low migration rates of tsetse between sites except between those situated in the Dubréka area, which seems to contain a widely distributed panmictic tsetse population (i.e. a population where mating occurs at random). Effective population sizes on Loos islands estimated with various techniques all converged to surprisingly small values. These values might be explained by a recent decrease in tsetse numbers on Kassa Island due to bauxite mining activities. But on the other sites, other explanations have to be found, including possible variance in reproductive success. Our genetic results suggest that different control strategies should be advised on the mainland (reduction in tsetse densities, no elimination) compared to the islands (total elimination feasible). This approach could be extended to many areas where vector control of Human and Animal Trypanosomoses is contemplated

Genotyping-by-Sequencing and Ecological Niche Modeling Illuminate Phylogeography, Admixture, and Pleistocene Range Dynamics in Quaking Aspen (Populus Tremuloides)

Populus tremuloides is the widest‐ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome‐wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal–Cascades (cluster 1), east‐slope Cascades–Sierra Nevadas–Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the “stable‐edge hypothesis” that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited “trailing‐edge” dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the “inland dispersal hypothesis” predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific‐coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable‐edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific‐coastal genetic lineage of quaking aspen

Is the central-marginal hypothesis a general rule? Evidence from three distributions of an expanding mangrove species, Avicennia germinans (L.)

The central-marginal hypothesis (CMH) posits that range margins exhibit less genetic diversity 16 and greater inter-population genetic differentiation compared to range cores. CMH predictions 17 are based on long-held ‘abundant-centre’ assumptions of a decline in ecological conditions and 18 abundances towards range margins. Although much empirical research has confirmed CMH, 19 exceptions remain almost as common. We contend that mangroves provide a model system to 20 test CMH that alleviates common confounding factors and may help clarify this lack of 21 consensus. Here, we document changes in black mangrove (Avicennia germinans) population 22 genetics with 12 nuclear microsatellite loci along three replicate coastlines in the United States 23 (only 2 of 3 conform to underlying ‘abundant-centre’ assumptions). We then test an implicit 24 prediction of CMH (reduced genetic diversity may constrain adaptation at range margins) by 25 measuring functional traits of leaves associated with cold tolerance, the climatic factor that 26 controls these mangrove distributional limits. CMH predictions were confirmed only along the 27 coastlines that conform to ‘abundant-centre’ assumptions and, in contrast to theory, range margin 28 A. germinans exhibited functional traits consistent with greater cold tolerance compared to range 29 cores. These findings support previous accounts that CMH may not be a general rule across 30 species and that reduced neutral genetic diversity at range margins may not be a constraint to 31 shifts in functional trait variation along climatic gradients