scholarly journals Species delimitation in the grey zone: introgression obfuscates phylogenetic inference and species boundaries in a cryptic frog complex (Ranidae: Pulchrana picturata)

2019 ◽  
Author(s):  
Kin Onn Chan ◽  
Carl R. Hutter ◽  
Perry L. Wood ◽  
L. Lee Grismer ◽  
Rafe M. Brown
Keyword(s):  
Species Delimitation ◽  
Intermediate Stage ◽  
Geographic Area ◽  
Species Boundaries ◽  
Grey Zone ◽  
Genetic Population ◽  
Phylogenetic Placement ◽  
Phylogenetic Discordance ◽  
Speciation Continuum

ABSTRACTAs molecular methods continue to elucidate genetic structure at increasingly finer resolutions, delimiting species in the grey zone of the speciation continuum is becoming more relevant in biodiversity research, especially in under-studied biodiversity hotspots such as Southeast Asia where new species are being described at an unprecedented rate. Obvious species at both ends of the speciation continuum have mostly been described and attention is now turning towards the “grey zone:” an intermediate stage in which species criteria are in conflict and boundaries between populations and species are less clear. This study demonstrates that widely-used criteria (phylogenetic placement, genetic divergence, phylogeny- and distance-based species delimitation methods) can overestimate species diversity/boundaries when introgression is present. However, a comprehensive species delimitation framework that considers spatial and genetic population structure, introgression, and the use of species delimitation methods based on parameter estimation, can provide a more accurate characterization of species boundaries in this grey zone. We applied this approach to a group of Southeast Asian frogs from the Pulchrana picturata Complex that exhibits continuous morphological variation and high genetic divergences. Results showed that introgression was rampant among Bornean populations, which led to phylogenetic discordance and an overestimation of species. We suspect that our results do not form an isolated case; and that introgression among cryptic populations, occurring continuously across a wide geographic area (e.g., the topographically complex island of Borneo, and Earth’s major continents), may be more common than previously thought.

scholarly journals Genetic Mapping and Molecular Characterization of a Broad-spectrum Phytophthora sojae Resistance Gene in Chinese Soybean

2019 ◽  
Vol 20 (8) ◽  
pp. 1809 ◽  
Author(s):  
Chao Zhong ◽  
Yinping Li ◽  
Suli Sun ◽  
Canxing Duan ◽  
Zhendong Zhu
Keyword(s):  
Genetic Mapping ◽  
Candidate Gene ◽  
Broad Spectrum ◽  
Genomic Region ◽  
Phytophthora Sojae ◽  
Genetic Population ◽  
Phytophthora Root Rot ◽  
Different Origins ◽  
Lrr Domain

Phytophthora root rot (PRR) causes serious annual soybean yield losses worldwide. The most effective method to prevent PRR involves growing cultivars that possess genes conferring resistance to Phytophthora sojae (Rps). In this study, QTL-sequencing combined with genetic mapping was used to identify RpsX in soybean cultivar Xiu94-11 resistance to all P. sojae isolates tested, exhibiting broad-spectrum PRR resistance. Subsequent analysis revealed RpsX was located in the 242-kb genomic region spanning the RpsQ locus. However, a phylogenetic investigation indicated Xiu94-11 carrying RpsX is distantly related to the cultivars containing RpsQ, implying RpsX and RpsQ have different origins. An examination of candidate genes revealed RpsX and RpsQ share common nonsynonymous SNP and a 144-bp insertion in the Glyma.03g027200 sequence encoding a leucine-rich repeat (LRR) region. Glyma.03g027200 was considered to be the likely candidate gene of RpsQ and RpsX. Sequence analyses confirmed that the 144-bp insertion caused by an unequal exchange resulted in two additional LRR-encoding fragments in the candidate gene. A marker developed based on the 144-bp insertion was used to analyze the genetic population and germplasm, and proved to be useful for identifying the RpsX and RpsQ alleles. This study implies that the number of LRR units in the LRR domain may be important for PRR resistance in soybean.

scholarly journals Determining Whether Geographic Origin and Potato Genotypes Shape the Population Structure of Phytophthora infestans in the Central Region of Colombia

2019 ◽  
Vol 109 (1) ◽  
pp. 145-154
Author(s):  
Sandra Catalina Chaves ◽  
María Camila Rodríguez ◽  
María Fernanda Mideros ◽  
Florencia Lucca ◽  
Carlos E. Ñústez ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Phytophthora Infestans ◽  
Central Region ◽  
Geographic Origin ◽  
Geographic Area ◽  
Potato Cultivars ◽  
Clonal Lineage ◽  
Host Genotype ◽  
Genetic Population

Pathogen variation plays an important role in the dynamics of infectious diseases. In this study, the genetic variation of 279 Phytophthora infestans isolates was assessed using a combination of 12 microsatellite simple-sequence repeat markers. Isolates were collected from 11 different potato cultivars in 11 different geographic localities of the central region of Colombia. The objective of this study was to determine whether populations were differentiated by host genotype or geographic origin. Within a single clonal lineage, EC-1, 76 genotypes were detected. An analysis of molecular variance attributed most of the variation to differences within host genotypes rather than among the host genotypes, suggesting that host cultivars do not structure the populations of the pathogen. Furthermore, the lack of a genetic population structure according to the host cultivar was confirmed by all of the analyses, including the Bayesian clustering analysis and the minimum spanning network that used the Bruvo genetic distance, which suggested that there are no significant barriers to gene flow for P. infestans among potato cultivars. According to the geographic origin, the populations of P. infestans were also not structured, and most of the variation among the isolates was attributed to differences within localities. Only some but not all localities in the north and west of the central region of Colombia showed some genetic differentiation from the other regions. The absence of sexual reproduction of this pathogen in Colombia was also demonstrated. Important insights are discussed regarding the genetic population dynamics of the P. infestans populations of the central region of Colombia that were provided by the results. In Colombia, there is a high genetic variation within the EC-1 clonal lineage with closely related genotypes, none dominant, that coexist in a wide geographic area and on several potato cultivars.

scholarly journals Characterization of Defatted Products Obtained from the Parmigiano–Reggiano Manufacturing Chain: Determination of Peptides and Amino Acids Content and Study of the Digestibility and Bioactive Properties

Foods ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 310 ◽  
Author(s):  
Sofie Buhler ◽  
Ylenia Riciputi ◽  
Giuseppe Perretti ◽  
Maria Fiorenza Caboni ◽  
Arnaldo Dossena ◽  
...  
Keyword(s):  
Amino Acids ◽  
Geographic Area ◽  
Ace Inhibition ◽  
Point Of View ◽  
Supercritical Co2 Extraction ◽  
Protected Designation Of Origin ◽  
Parmigiano Reggiano ◽  
Manufacturing Chain

Parmigiano–Reggiano (PR) is a worldwide known Italian, long ripened, hard cheese. Its inclusion in the list of cheeses bearing the protected designation of origin (PDO, EU regulation 510/2006) poses restrictions to its geographic area of production and its technological characteristics. To innovate the Parmigiano–Reggiano (PR) cheese manufacturing chain from the health and nutritional point of view, the output of defatted PR is addressed. Two defatting procedures (Soxhlet, and supercritical CO2 extraction) were tested, and the obtained products were compared in the composition of their nitrogen fraction, responsible for their nutritional, organoleptic, and bioactive functions. Free amino acids were quantified, and other nitrogen compounds (peptides, proteins, and non-proteolytic aminoacyl derivatives) were identified in the extracts and the mixtures obtained after simulated gastrointestinal digestion. Moreover, antioxidant and angiotensin converting enzyme (ACE) inhibition capacities of the digests were tested. Results obtained from the molecular and biofunctional characterization of the nitrogen fraction, show that both the defatted products keep the same nutritional properties of the whole cheese.

Surge Pricing and Its Spatial Supply Response

2020 ◽  
Author(s):  
Omar Besbes ◽  
Francisco Castro ◽  
Ilan Lobel
Keyword(s):  
Supply And Demand ◽  
Optimal Solution ◽  
Geographic Area ◽  
Equilibrium Constraints ◽  
Supply Response ◽  
Infinite Dimensional ◽  
Travel Costs ◽  
Spatial Decomposition ◽  
Local Characterization

We consider the pricing problem faced by a revenue-maximizing platform matching price-sensitive customers to flexible supply units within a geographic area. This can be interpreted as the problem faced in the short term by a ride-hailing platform. We propose a two-dimensional framework in which a platform selects prices for different locations and drivers respond by choosing where to relocate, in equilibrium, based on prices, travel costs, and driver congestion levels. The platform’s problem is an infinite-dimensional optimization problem with equilibrium constraints. We elucidate structural properties of supply equilibria and the corresponding utilities that emerge and establish a form of spatial decomposition, which allows us to localize the analysis to regions of movement. In turn, uncovering an appropriate knapsack structure to the platform’s problem, we establish a crisp local characterization of the optimal prices and the corresponding supply response. In the optimal solution, the platform applies different treatments to different locations. In some locations, prices are set so that supply and demand are perfectly matched; overcongestion is induced in other locations, and some less profitable locations are indirectly priced out. To obtain insights on the global structure of an optimal solution, we derive in quasi-closed form the optimal solution for a family of models characterized by a demand shock. The optimal solution, although better balancing supply and demand around the shock, quite interestingly also ends up inducing movement away from it. This paper was accepted by David Simchi-Levi, optimization.

Multiple Small Angle Neutron Scattering Characterization of the Densification of Alumina

1989 ◽  
Vol 166 ◽  
Author(s):  
S. Krueger ◽  
G.C. Long ◽  
R.A. Page
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Pore Radius ◽  
Intermediate Stage ◽  
Sample Density ◽  
Microstructure Morphology ◽  
Interconnected Pore ◽  
Effective Pore Radius

ABSTRACTMultiple small angle neutron scattering (MSANS) was used to follow the evolution of the pore size distribution in α-Al2O3through the intermediate and final stages of sintering. This technique makes it possible to determine microstructure morphology in the 0.08 to 10 μm size regime under conditions where the total scattering cross-section is dominated by elastic incoherent multiple scattering, as is often the case for ceramics. The MSANS results indicate an initial decrease in the effective pore radius from 0.19 μm at 57% of theoretical density (TD) to 0.17 μm at 79% TD. As the sample density further increased, there was a transition region after which the effective pore radius grew rapidly to ≤0.5 μm at 98% TD. Standard Porod analysis on scattering by the same samples also indicates a transition between the intermediate and final stages of processing. Both sets of results support a topological model of sintering in which the interconnected pore network in the intermediate stage of sintering decays in a stable manner. The pores become fewer, while retaining the same diameter, as densification proceeds. In the final stage, isolated pores remain.

scholarly journals Phylogenetic placement and characterization of a new alpha-2 proteobacterium isolated from a patient with sepsis.

1997 ◽  
Vol 35 (8) ◽  
pp. 1988-1995 ◽  
Author(s):  
G Blomqvist ◽  
L Wesslén ◽  
C Påhlson ◽  
E Hjelm ◽  
B Pettersson ◽  
...  
Keyword(s):  
Phylogenetic Placement
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