The evolutionary history of wild, domesticated, and feral brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions

Dispersion of finite-size particles probing inhomogeneous and anisotropic turbulence

A series of 8 laboratory experiments was used to investigate the dynamics of a few almost neutrally-buoyant finite-size particles in the entire volume of a rectangular tank open to air and filled with water. Stirring was achieved by a cylinder executing a two-dimensional periodic Lissajoux figure. The rate and direction of stirring by the cylinder was varied. The particle motions were analyzed using a tracking method developed for the experimental design. The Reynolds number associated with the large-scale stirring motion was in a turbulent range of [5,693-11,649] across all experiments. The absence of stirring in the direction of the cylinder axis, the constant interference of the cylinder with the eddies and the presence of walls and the free-surface resulted in a flow that was both inhomogeneous and anisotropic as recorded by the particle motion. Despite these unusual conditions, the single-particle dispersion across all experiments could be seen to follow a ballistic regime until about two-fifths of the particle Lagrangian velocity auto-correlation time T_L. It was followed by a brief diffusive regime between T_L and 2.5 T_L, after which the presence of the boundaries prevented further dispersion. Such evolution is consistent with classic predictions for fluid tracer dispersion in homogeneous and isotropic turbulence. Particle-pair dispersion was more complex. Both the fixed time-averaged and length-scale-dependent particle-pair dispersion rates averaged across pairs showed the ballistic dispersion regime, whereas the subsequent diffusive regime was better borne out by the length-scale-dependent particle-pair dispersion. A super-diffusive Richardson regime was not unmistakably detected. Substantial variability was however found across the different pairs of particles, which was linked to differences in the decorrelation time of the velocity difference as a result of the inhomogeneity of the turbulence. For short initial separations, some particle pairs had a better separation of the time scales delimiting the ballistic and diffusive regimes and showed hints of a brief Richardson regime

Multi-trait genome-wide association study identifies new loci associated with optic disc parameters

A new avenue of mining published genome-wide association studies includes the joint analysis of related traits. The power of this approach depends on the genetic correlation of traits, which reflects the number of pleiotropic loci, i.e. genetic loci influencing multiple traits. Here, we applied new meta-analyses of optic nerve head (ONH) related traits implicated in primary open-angle glaucoma (POAG); intraocular pressure and central corneal thickness using Haplotype reference consortium imputations. We performed a multi-trait analysis of ONH parameters cup area, disc area and vertical cup-disc ratio. We uncover new variants; rs11158547 in PPP1R36-PLEKHG3 and rs1028727 near SERPINE3 at genome-wide significance that replicate in independent Asian cohorts imputed to 1000 Genomes. At this point, validation of these variants in POAG cohorts is hampered by the high degree of heterogeneity. Our results show that multi-trait analysis is a valid approach to identify novel pleiotropic variants for ONH

Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error.

Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia

Supplementary Material for: Policy Decisions on Endocrine Disruptors Should Be Based on Science across Disciplines: A Response to Dietrich et al.

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