Crop Plants as Models for Understanding Plant Adaptation and Diversification

Since the time of Darwin, biologists have understood the promise of crop plants and their wild relatives for providing insight into the mechanisms of phenotypic evolution. The intense selection imposed by our ancestors during plant domestication and subsequent crop improvement has generated remarkable transformations of plant phenotypes. Unlike evolution in natural settings, descendent and antecedent conditions for crop plants are often both extant, providing opportunities for direct comparisons through crossing and other experimental approaches. Moreover, since domestication has repeatedly generated a suite of domestication syndrome traits that are shared among crops, opportunities exist for gaining insight into the genetic and developmental mechanisms that underlie parallel adaptive evolution. Advances in our understanding of the genetic architecture of domestication-related traits have emerged from combining powerful molecular technologies with advanced experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies may be combined with high-throughput evaluations of the various omics involved in trait transformation, revealing a diversity of underlying causative mutations affecting phenotypes and their downstream propagation through biological networks. We summarize the state of our knowledge of the mutational spectrum that generates phenotypic novelty in domesticated plant species, and our current understanding of how domestication can reshape gene expression networks and emergent phenotypes. An exploration of traits that have been subject to similar selective pressures across crops (e.g., flowering time) suggests that a diversity of targeted genes and causative mutational changes can underlie parallel adaptation in the context of crop evolution

Population genetics and origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus; Amaranthaceae)

Premise of the study—The evolution of invasiveness has been extensively studied in natural ecosystems; however, far less is known about the evolution of agricultural invasiveness, despite the major economic impact of weeds on crop productivity. Examining the population structure of recently arisen weeds can provide insights into evolutionary avenues to invasion of agroecosystems. Weeds that originate from wild plants are the most common yet least frequently studied type of agricultural invasive. Here we address several questions about the origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus), which invaded corn and soy fields in the Midwestern U.S. in the 20th century. Methods—We genotyped 38 populations from across the species range with 10 microsatellite markers, and used these data to assess genetic diversity and population structure within and outside the geographical region where waterhemp is agriculturally problematic. Key Results—We found evidence for two ancestral genetic lineages in our data, supporting the hypothesis that A. tuberculatus was diverging into two evolutionary lineages prior to the 20th century. However, we found no support for the hypothesis that agricultural weed populations arose from admixture of these two lineages after secondary contact. Our data suggest that eastward movement of the western genetic lineage, facilitated by changing agricultural practices, is the source of the agricultural invasion of waterhemp. Conclusions—This research demonstrates that agricultural invasion by native, wild plant species can proceed via different evolutionary trajectories from weeds related to domesticated plants, which has implications for evolutionary biology and weed control

The presence of coconut in southern Panama in pre-Columbian times: Clearing up the confusion

Background The pre-Columbian presence of coconut on the Pacific coast of Panama is attested by a number of independent written accounts. However, recent papers question their accuracy and conclude that coconut was introduced to the region by the Spaniards after their conquests. Scope In order to examine the value of such claims, an extensive search was conducted of the relevant historical accounts of coconut in America and in the Orient. Key Results The Spanish chronicler Oviedo (1478-1557) is found to have effectively used fruit and seed size to distinguish coconut from other palms. In addition, it is shown that he has been inaccurately faulted with incorrectly representing a cluster of coconuts. The original drawing, a cluster of a native Bactris, was in the marginalia and was only assigned to coconut after Oviedo's death. Finally, the location is identified of a coastal Panamanian site described by Pedro Mártir de Anglería and where tidal dispersal of coconuts was observed. Conclusions This previously overlooked evidence confirms the pre-historical presence of coconut in Panama. Genetic data indicate that it must have been brought there directly or indirectly from the Philippines. But when, where and by whom remains a subject of research. Further molecular marker studies, computer simulation of natural drift and archaeological research could contribute to this research. (Résumé d'auteur

Long-term balancing selection at the Phosphorus Starvation Tolerance 1 (PSTOL1) locus in wild, domesticated and weedy rice (Oryza)

Dry Shoot Weights of PSTOL1 genotypes grown in low and high phosphorus conditions. Plants were measured after 21 days in high phosphorus (black) and low phosphorus (grey) media. (PDF 72 kb

Novel Phr1 mutations and the evolution of phenol reaction variation

Summary • Red rice, a major agricultural weed, is phenotypically diverse and possesses traits that are similar to both wild and cultivated rice. The genetic resources available for rice make it possible to examine the molecular basis and evolution of traits characterizing this weed. Here, we assess the phenol reaction -a classical trait for distinguishing among cultivated rice varieties -in red rice at the phenotypic and molecular levels. • We phenotyped more than 100 US weed samples for the phenol reaction and sequenced the underlying Phr1 locus in a subset of samples. Data were analyzed in combination with previously published Phr1 data for cultivated rice. • Most weed accessions (96.3%) are positive for the phenol reaction, and samples with a negative response carry loss-of-function alleles that are rare or heretofore undocumented. One such allele may have evolved through mutational convergence of a 1-bp frameshift insertion. Haplotype sharing between red rice and US cultivars suggests occasional crop-weed hybridization. • Our discovery of previously undocumented nonfunctional phr1 alleles suggests that there are likely to be other loss-of-function mutations segregating in Oryza sativa around the world. Red rice may provide a useful study system for understanding the adaptive significance of Phr1 variation in agricultural settings

Probing open- and closed-channel p-wave resonances

We study the near-threshold molecular and collisional physics of a strong $^{40}$K p-wave Feshbach resonance through a combination of measurements, numerical calculations, and modeling. Dimer spectroscopy employs both radio-frequency spin-flip association in the MHz band and resonant association in the kHz band. Systematic uncertainty in the measured binding energy is reduced by a model that includes both the Franck-Condon overlap amplitude and inhomogeneous broadening. Coupled-channels calculations based on mass-scaled $^{39}$K potentials compare well to the observed binding energies and also reveal a low-energy p-wave shape resonance in the open channel. Contrary to conventional expectation, we observe a nonlinear variation of the binding energy with magnetic field, and explain how this arises from the interplay of the closed-channel ramping state with the near-threshold shape resonance in the open channel. We develop an analytic two-channel model that includes both resonances as well as the dipole-dipole interactions which, we show, become important at low energy. Using this parameterization of the energy dependence of the scattering phase, we can classify the studied $^{40}$K resonance as broad. Throughout the paper, we compare to the well understood s-wave case, and discuss the significant role played by van der Waals physics. The resulting understanding of the dimer physics of p-wave resonances provides a solid foundation for future exploration of few- and many-body orbital physics.Comment: v4: new appendi

Comparison of Clinician Suspicion Versus a Clinical Prediction Rule in Identifying Children at Risk for Intra‐abdominal Injuries After Blunt Torso Trauma

ObjectivesEmergency department (ED) identification and radiographic evaluation of children with intra‐abdominal injuries who need acute intervention can be challenging. To date, it is unclear if a clinical prediction rule is superior to unstructured clinician judgment in identifying these children. The objective of this study was to compare the test characteristics of clinician suspicion with a derived clinical prediction rule to identify children at risk of intra‐abdominal injuries undergoing acute intervention following blunt torso trauma.MethodsThis was a planned subanalysis of a prospective, multicenter observational study of children (50% prior to knowledge of abdominal computed tomography (CT) scanning (if performed). Intra‐abdominal injuries undergoing acute intervention were defined by a therapeutic laparotomy, angiographic embolization, blood transfusion for abdominal hemorrhage, or intravenous fluid administration for 2 or more days in those with pancreatic or gastrointestinal injuries. Patients were considered to be positive for clinician suspicion if suspicion was documented as ≥1%. Suspicion ≥ 1% was compared to the presence of any variable in the prediction rule for identifying children with intra‐abdominal injuries undergoing acute intervention.ResultsClinicians recorded their suspicion in 11,919 (99%) of 12,044 patients enrolled in the parent study. Intra‐abdominal injuries undergoing acute intervention were diagnosed in 203 (2%) patients. Abdominal CT scans were obtained in the ED in 2,302 of the 2,667 (86%, 95% confidence interval [CI] = 85% to 88%) enrolled patients with clinician suspicion ≥1% and in 3,016 of the 9,252 (33%, 95% CI = 32% to 34%) patients with clinician suspicion  50% previamente a conocer la tomografía computarizada (TC) abdominal (si fue realizada). La LIA con necesidad de intervención urgente se definió como laparotomía terapéutica, embolización angiográfica, transfusión de sangre por hemorragia intrabdominal o administración de fluidos intravenosos durante 2 o más días en aquéllos con lesiones pancreáticas o gastrointestinales. Los pacientes se consideraron positivos para la sospecha clínica si la sospecha se documentó como ≥1%. La sospecha > 1% se comparó con la presencia de cualquier variable en la regla de predicción para la identificación de niños con LIA con necesidad de una intervención urgente.ResultadosLos clínicos documentaron su sospecha en 11.919 (99%) de los 12.044 pacientes incluidos en el estudio original. La LIA con necesidad de intervención urgente se diagnosticó en 203 (2%) pacientes. Las TC abdominales se obtuvieron en el SU en 2.302 de los 2.667 pacientes (86%, IC95% = 85% a 88%) incluidos con sospecha clínica ≥1%; y en 3.016 de los 9.252 pacientes (33%, IC95% = 32% a 34%) con sospecha clínica < 1%. La sensibilidad de la regla de predicción para LIA con necesidad de intervención aguda fue mayor que la sospecha clínica ≥1% (197 de 203, 97,0%, IC95% = 93,7% a 98,9%, frente a 168 de 203, 82,8%, IC95% = 76,9% a 87,7%, respectivamente; diferencia de 14,2%, IC95% = 8,6% a 20,0%). La especificidad de la regla de predicción, sin embargo, fue menor que la sospecha clínica (4,979 de los 11.716, 42,5%, IC95% = 41,6% a 43,4%, frente a 9,217 de los 11.716, 78,7%, IC95% = 77,9% a 79,4%, respectivamente; diferencia de –36,2%, IC95% = –37,3% a –35,0%). Treinta y cinco de los pacientes con sospecha clínica < 1% (0,4%, IC95% = 0,3% a 0,5%) tuvieron LIA con necesidad de intervención urgente.ConclusionesLa regla de predicción clínica derivada tuvo una sensibilidad mayor de forma significativa, pero menor especificidad que la sospecha clínica para la identificación de niños con necesidad de una intervención urgente. La mayor especificidad de la sospecha clínica, sin embargo, no se tradujo en la práctica clínica, ya que los clínicos obtuvieron más frecuentemente TC abdominales en los pacientes que consideraron de muy bajo riesgo. Si se validase, esta regla de predicción puede ayudar en la toma de decisiones clínicas sobre el uso de TC abdominal en los niños con traumatismo torácico cerrado.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113736/1/acem12739.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/113736/2/acem12739_am.pd

Convergence towards a European strategic culture? A constructivist framework for explaining changing norms.

The article contributes to the debate about the emergence of a European strategic culture to underpin a European Security and Defence Policy. Noting both conceptual and empirical weaknesses in the literature, the article disaggregates the concept of strategic culture and focuses on four types of norms concerning the means and ends for the use of force. The study argues that national strategic cultures are less resistant to change than commonly thought and that they have been subject to three types of learning pressures since 1989: changing threat perceptions, institutional socialization, and mediatized crisis learning. The combined effect of these mechanisms would be a process of convergence with regard to strategic norms prevalent in current EU countries. If the outlined hypotheses can be substantiated by further research the implications for ESDP are positive, especially if the EU acts cautiously in those cases which involve norms that are not yet sufficiently shared across countries