Observation and theory of X-ray mirages.

PubMed

Magnitskiy, Sergey; Nagorskiy, Nikolay; Faenov, Anatoly; Pikuz, Tatiana; Tanaka, Mamoko; Ishino, Masahiko; Nishikino, Masaharu; Fukuda, Yuji; Kando, Masaki; Kawachi, Tetsuya; Kato, Yoshiaki

2013-01-01

The advent of X-ray lasers allowed the realization of compact coherent soft X-ray sources, thus opening the way to a wide range of applications. Here we report the observation of unexpected concentric rings in the far-field beam profile at the output of a two-stage plasma-based X-ray laser, which can be considered as the first manifestation of a mirage phenomenon in X-rays. We have developed a method of solving the Maxwell-Bloch equations for this problem, and find that the experimentally observed phenomenon is due to the emergence of X-ray mirages in the plasma amplifier, appearing as phase-matched coherent virtual point sources. The obtained results bring a new insight into the physical nature of amplification of X-ray radiation in laser-induced plasma amplifiers and open additional opportunities for X-ray plasma diagnostics and extreme ultraviolet lithography.

West Magnesia Canyon Channel, City of Rancho Mirage, Riverside County, California. Detailed Project Report. Rancho Mirage Flood Control. Technical Appendixes.

DTIC Science & Technology

1983-12-01

Maximum Site site length Earthquake Accelerations Fault (miles) (miles) (Magnitude) in Bedrock (g)* Agua Caliente 32 50 7.25 0.13 Calico-Newberry 56 50...disturbed samples of representative materials were - obtained for laboratory testing. Seventeen inr- situ density tests were * conducted in the excavated...disturbed samples of representative materials were obtained for - --.-- laboratory testing. Four in- situ density tests were conducted in the trenches by the

Geologic map database of the El Mirage Lake area, San Bernardino and Los Angeles Counties, California

USGS Publications Warehouse

Miller, David M.; Bedford, David R.

2000-01-01

This geologic map database for the El Mirage Lake area describes geologic materials for the dry lake, parts of the adjacent Shadow Mountains and Adobe Mountain, and much of the piedmont extending south from the lake upward toward the San Gabriel Mountains. This area lies within the western Mojave Desert of San Bernardino and Los Angeles Counties, southeastern California. The area is traversed by a few paved highways that service the community of El Mirage, and by numerous dirt roads that lead to outlying properties. An off-highway vehicle area established by the Bureau of Land Management encompasses the dry lake and much of the land north and east of the lake. The physiography of the area consists of the dry lake, flanking mud and sand flats and alluvial piedmonts, and a few sharp craggy mountains. This digital geologic map database, intended for use at 1:24,000-scale, describes and portrays the rock units and surficial deposits of the El Mirage Lake area. The map database was prepared to aid in a water-resource assessment of the area by providing surface geologic information with which deepergroundwater-bearing units may be understood. The area mapped covers the Shadow Mountains SE and parts of the Shadow Mountains, Adobe Mountain, and El Mirage 7.5-minute quadrangles. The map includes detailed geology of surface and bedrock deposits, which represent a significant update from previous bedrock geologic maps by Dibblee (1960) and Troxel and Gunderson (1970), and the surficial geologic map of Ponti and Burke (1980); it incorporates a fringe of the detailed bedrock mapping in the Shadow Mountains by Martin (1992). The map data were assembled as a digital database using ARC/INFO to enable wider applications than traditional paper-product geologic maps and to provide for efficient meshing with other digital data bases prepared by the U.S. Geological Survey's Southern California Areal Mapping Project.

Deflected mirage mediation: a phenomenological framework for generalized supersymmetry breaking.

PubMed

Everett, Lisa L; Kim, Ian-Woo; Ouyang, Peter; Zurek, Kathryn M

2008-09-05

We present a general phenomenological framework for dialing between gravity mediation, gauge mediation, and anomaly mediation. The approach is motivated from recent developments in moduli stabilization, which suggest that gravity mediated terms can be effectively loop suppressed and thus comparable to gauge and anomaly mediated terms. The gauginos exhibit a mirage unification behavior at a "deflected" scale, and gluinos are often the lightest colored sparticles. The approach provides a rich setting in which to explore generalized supersymmetry breaking at the CERN Large Hadron Collider.

[Science and ethics, therapeutic misconception and mirage].

PubMed

Raymond, J; Long, H

2008-12-01

Medical practice changes constantly. Ethical imperatives are however incorrigible. How can we reconcile ethics, practice and progress? Some bioethicians argue that research and care should be disentangled to minimize the 'therapeutic misconception', a clinical propensity to believe that patients are the object of medical care, while in fact they are the subjects of a scientific experiment. On the contrary, we believe that clinical research should be an integral part of the good practice. A divorce between research and clinical practice leads to an incorrigible medicine, liable to the therapeutic mirage, that is the false belief that everything modern medicine can offer has been proved beneficial. But both therapeutic misconception and mirage are possible because of a misunderstanding of either research or clinical practice. In this essay we review ethical principles behind clinical trial methodology and attempt to reconcile ethics, science and clinical practice. Not only should clinical research be integrated to the good practice of medicine, it should also be part of training in our specialty.

Two-baryon systems from HAL QCD method and the mirage in the temporal correlation of the direct method

NASA Astrophysics Data System (ADS)

Iritani, Takumi

2018-03-01

Both direct and HAL QCD methods are currently used to study the hadron interactions in lattice QCD. In the direct method, the eigen-energy of two-particle is measured from the temporal correlation. Due to the contamination of excited states, however, the direct method suffers from the fake eigen-energy problem, which we call the "mirage problem," while the HAL QCD method can extract information from all elastic states by using the spatial correlation. In this work, we further investigate systematic uncertainties of the HAL QCD method such as the quark source operator dependence, the convergence of the derivative expansion of the non-local interaction kernel, and the single baryon saturation, which are found to be well controlled. We also confirm the consistency between the HAL QCD method and the Lüscher's finite volume formula. Based on the HAL QCD potential, we quantitatively confirm that the mirage plateau in the direct method is indeed caused by the contamination of excited states.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parekh, V; Jacobs, MA

Purpose: Multiparametric radiological imaging is used for diagnosis in patients. Potentially extracting useful features specific to a patient’s pathology would be crucial step towards personalized medicine and assessing treatment options. In order to automatically extract features directly from multiparametric radiological imaging datasets, we developed an advanced unsupervised machine learning algorithm called the multidimensional imaging radiomics-geodesics(MIRaGe). Methods: Seventy-six breast tumor patients underwent 3T MRI breast imaging were used for this study. We tested the MIRaGe algorithm to extract features for classification of breast tumors into benign or malignant. The MRI parameters used were T1-weighted, T2-weighted, dynamic contrast enhanced MR imaging (DCE-MRI)more » and diffusion weighted imaging(DWI). The MIRaGe algorithm extracted the radiomics-geodesics features (RGFs) from multiparametric MRI datasets. This enable our method to learn the intrinsic manifold representations corresponding to the patients. To determine the informative RGF, a modified Isomap algorithm(t-Isomap) was created for a radiomics-geodesics feature space(tRGFS) to avoid overfitting. Final classification was performed using SVM. The predictive power of the RGFs was tested and validated using k-fold cross validation. Results: The RGFs extracted by the MIRaGe algorithm successfully classified malignant lesions from benign lesions with a sensitivity of 93% and a specificity of 91%. The top 50 RGFs identified as the most predictive by the t-Isomap procedure were consistent with the radiological parameters known to be associated with breast cancer diagnosis and were categorized as kinetic curve characterizing RGFs, wash-in rate characterizing RGFs, wash-out rate characterizing RGFs and morphology characterizing RGFs. Conclusion: In this paper, we developed a novel feature extraction algorithm for multiparametric radiological imaging. The results demonstrated the power of the MIRaGe algorithm at automatically discovering useful feature representations directly from the raw multiparametric MRI data. In conclusion, the MIRaGe informatics model provides a powerful tool with applicability in cancer diagnosis and a possibility of extension to other kinds of pathologies. NIH (P50CA103175, 5P30CA006973 (IRAT), R01CA190299, U01CA140204), Siemens Medical Systems (JHU-2012-MR-86-01) and Nivida Graphics Corporation.« less

Preliminary hydrogeologic assessment near the boundary of the Antelope Valley and El Mirage Valley groundwater basins, California

USGS Publications Warehouse

Stamos, Christina L.; Christensen, Allen H.; Langenheim, Victoria

2017-07-19

The increasing demands on groundwater for water supply in desert areas in California and the western United States have resulted in the need to better understand groundwater sources, availability, and sustainability. This is true for a 650-square-mile area that encompasses the Antelope Valley, El Mirage Valley, and Upper Mojave River Valley groundwater basins, about 50 miles northeast of Los Angeles, California, in the western part of the Mojave Desert. These basins have been adjudicated to ensure that groundwater rights are allocated according to legal judgments. In an effort to assess if the boundary between the Antelope Valley and El Mirage Valley groundwater basins could be better defined, the U.S. Geological Survey began a cooperative study in 2014 with the Mojave Water Agency to better understand the hydrogeology in the area and investigate potential controls on groundwater flow and availability, including basement topography.Recharge is sporadic and primarily from small ephemeral washes and streams that originate in the San Gabriel Mountains to the south; estimates range from about 400 to 1,940 acre-feet per year. Lateral underflow from adjacent basins has been considered minor in previous studies; underflow from the Antelope Valley to the El Mirage Valley groundwater basin has been estimated to be between 100 and 1,900 acre-feet per year. Groundwater discharge is primarily from pumping, mostly by municipal supply wells. Between October 2013 and September 2014, the municipal pumpage in the Antelope Valley and El Mirage Valley groundwater basins was reported to be about 800 and 2,080 acre-feet, respectively.This study was motivated by the results from a previously completed regional gravity study, which suggested a northeast-trending subsurface basement ridge and saddle approximately 3.5 miles west of the boundary between the Antelope Valley and El Mirage Valley groundwater basins that might influence groundwater flow. To better define potential basement structures that could affect groundwater flow between the groundwater basins in the study area, gravity data were collected using more closely spaced measurements in September 2014. Groundwater-level data was gathered and collected from March 2014 through March 2015 to determine depth to water and direction of groundwater flow. The gravity and groundwater-level data showed that the saturated thickness of the alluvium was about 2,000 feet thick to the east and about 130 feet thick above the northward-trending basement ridge near Llano, California. Although it was uncertain whether the basement ridge affects the groundwater system, a potential barrier to groundwater flow could be created if the water table fell below the altitude of the basement ridge, effectively causing the area to the west of the basement ridge to become hydraulically isolated from the area to the east. In addition, the direction of regional-groundwater flow likely will be influenced by future changes in the number and distribution of pumping wells and the thickness of the saturated alluvium from which water is withdrawn. Three-dimensional animations were created to help visualize the relation between the basins’ basement topography and the groundwater system in the area. Further studies that could help to more accurately define the basins and evaluate the groundwater-flow system include exploratory drilling of multi-depth monitoring wells; collection of depth-dependent water-quality samples; and linking together existing, but separate, groundwater-flow models from the Antelope Valley and El Mirage Valley groundwater basins into a single, calibrated groundwater-flow model.

High-temperature MIRAGE XL (LFRA) IRSP system development

NASA Astrophysics Data System (ADS)

McHugh, Steve; Franks, Greg; LaVeigne, Joe

2017-05-01

The development of very-large format infrared detector arrays has challenged the IR scene projector community to develop larger-format infrared emitter arrays. Many scene projector applications also require much higher simulated temperatures than can be generated with current technology. This paper will present an overview of resistive emitterbased (broadband) IR scene projector system development, as well as describe recent progress in emitter materials and pixel designs applicable for legacy MIRAGE XL Systems to achieve apparent temperatures >1000K in the MWIR. These new high temperature MIRAGE XL (LFRA) Digital Emitter Engines (DEE) will be "plug and play" equivalent with legacy MIRAGE XL DEEs, the rest of the system is reusable. Under the High Temperature Dynamic Resistive Array (HDRA) development program, Santa Barbara Infrared Inc. (SBIR) is developing a new infrared scene projector architecture capable of producing both very large format (>2k x 2k) resistive emitter arrays and improved emitter pixel technology capable of simulating very high apparent temperatures. During earlier phases of the program, SBIR demonstrated materials with MWIR apparent temperatures in excess of 1500 K. These new emitter materials can be utilized with legacy RIICs to produce pixels that can achieve 7X the radiance of the legacy systems with low cost and low risk. A 'scalable' Read-In Integrated Circuit (RIIC) is also being developed under the same HDRA program to drive the high temperature pixels. This RIIC will utilize through-silicon via (TSV) and Quilt Packaging (QP) technologies to allow seamless tiling of multiple chips to fabricate very large arrays, and thus overcome the yield limitations inherent in large-scale integrated circuits. These quilted arrays can be fabricated in any N x M size in 512 steps.

An X-ray diffractometer using mirage diffraction

PubMed Central

Fukamachi, Tomoe; Jongsukswat, Sukswat; Ju, Dongying; Negishi, Riichirou; Hirano, Keiichi; Kawamura, Takaaki

2014-01-01

Some characteristics are reported of a triple-crystal diffractometer with a (+, −, +) setting of Si(220) using mirage diffraction. The first crystal is flat, while the second and third crystals are bent. Basically, the first crystal is used as a collimator, the second as a monochromator and the third as the sample. The third crystal also works as an analyzer. The advantages of this diffractometer are that its setup is easy, its structure is simple, the divergence angle from the second crystal is small and the energy resolution of the third crystal is high, of the order of sub-meV. PMID:25242911

Food mirages: geographic and economic barriers to healthful food access in Portland, Oregon.

PubMed

Breyer, Betsy; Voss-Andreae, Adriana

2013-11-01

This paper investigated the role of grocery store prices in structuring food access for low-income households in Portland, Oregon. We conducted a detailed healthful foods market basket survey and developed an index of store cost based on the USDA Thrifty Food Plan. Using this index, we estimated the difference in street-network distance between the nearest low-cost grocery store and the nearest grocery store irrespective of cost. Spatial regression of this metric in relation to income, poverty, and gentrification at the census tract scale lead to a new theory regarding food access in the urban landscape. Food deserts are sparse in Portland, but food mirages are abundant, particularly in gentrifying areas where poverty remains high. In a food mirage, grocery stores are plentiful but prices are beyond the means of low-income households, making them functionally equivalent to food deserts in that a long journey to obtain affordable, nutritious food is required in either case. Results suggested that evaluation of food environments should, at a minimum, consider both proximity and price in assessing healthy food access for low-income households. © 2013 Elsevier Ltd. All rights reserved.

Development of a work improvement checklist for occupational mental health focused on requests from workers.

PubMed

Tahara, Hiroyuki; Yamada, Tatsuji; Nagafuchi, Keiko; Shirakawa, Chie; Suzuki, Kiyomi; Mafune, Kosuke; Kubota, Shinya; Hiro, Hisanori; Mishima, Norio; Nagata, Shoji

2009-01-01

To develop tools offering definite orientation for managers and employees to support their work improvement through occupational mental health. This research was a part of the Mental Health Improvement & Reinforcement Study (MIR study), conducted from October 2004 to March 2006. We developed a trial version named the Kaizen Check List (KCL) by referring to problem solving methods for quality management. Then we improved it for a formal version named MIR Research of Recognition (MIRROR). A feedback form named MIR Action Guidance (MIRAGe) was also developed. We analyzed data from 1,953 respondents at five manufacturing enterprises in Japan using MIRROR and the Brief Job Stress Questionnaire (BJSQ) to determine whether or not the workers requesting work improvement had more stress than other workers. The KCL had 47 items, which indicated desirable working conditions for mental health at work, and four answer categories. MIRROR has 45 selected items and improved answer categories. MIRAGe displays the results of MIRROR and step-by-step guidance for work improvement. Respondents with request had significantly higher scores in stressor and lower scores in buffer factors compared with respondents without request in many items of MIRROR. A combinational use of MIRROR and stress scales is useful for finding worksites with high risk factors for mental health and for directing focus on work improvement at these worksites according to workers' requests.

West Magnesia Canyon Channel, City of Rancho Mirage, Riverside County, California. Detailed Project Report. RANCHO MIRAGE, Flood Control. Main Report and EIS (Environmental Impact Statement) with Public Involvement and Environmental Appendixes.

DTIC Science & Technology

1983-12-01

bt .I~~ !, i 1 I - Iid 4 , 1h it " -;uai ml los1 C . . s t U I~ ( -~ S p jugI;I 1 iI V, U hanf i . I t I ( r, t hr ugh th. st uIdv ar tI. tirt I), ,i...sediment deposition during high flows. This alternative was deleted from further consideration due to the potential for levee failure as a result of...depth or width of the channel. This alternative has been deleted from further consideration for this reae. ....... .. .. . . =-- , - ~-- 13-i ! I

Who owns the recyclables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parker, B.

On March 31, the California Supreme Court decided the much awaited Rancho Mirage'' case (Waste Management of the Desert, Inc., and the City of Rancho Mirage v. Palm Springs Recycling Center, Inc.), and held that the California Integrated Waste Management Act of 1989 does not allow an exclusive franchise for the collection of recyclables not discarded by their owner.'' This ends a three-year slugfest between secondary materials processors in the state and municipalities and their franchised garbage haulers who also collect and process recyclables as part of their exclusive arrangement. Central to this nationally-watched litigation is a most fundamental questionmore » in waste management: at what point in time do articles in the solid waste stream become actual or potentially valuable secondary materials« less

Strain distribution in an Si single crystal measured by interference fringes of X-ray mirage diffraction

PubMed Central

Jongsukswat, Sukswat; Fukamachi, Tomoe; Ju, Dongying; Negishi, Riichirou; Hirano, Keiichi; Kawamura, Takaaki

2013-01-01

In X-ray interference fringes accompanied by mirage diffraction, variations have been observed in the spacing and position of the fringes from a plane-parallel Si single crystal fixed at one end as a function of distance from the incident plane of the X-rays to the free crystal end. The variations can be explained by distortion of the sample crystal due to gravity. From the variations and positions of the fringes, the strain gradient of the crystal has been determined. The distribution of the observed strain agrees with that expected from rod theory except for residual strain. When the distortion is large, the observed strain distribution does not agree with that expected from rod theory. PMID:24068841

Transport mirages in single-molecule devices

NASA Astrophysics Data System (ADS)

Gaudenzi, R.; Misiorny, M.; Burzurí, E.; Wegewijs, M. R.; van der Zant, H. S. J.

2017-03-01

Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic, and optical properties. At the single-molecule level, two major complementary ways to explore these properties are molecular quantum-dot structures and scanning probes. This article outlines comprehensive principles of electron-transport spectroscopy relevant to both these approaches and presents a new, high-resolution experiment on a high-spin single-molecule junction exemplifying these principles. Such spectroscopy plays a key role in further advancing our understanding of molecular and atomic systems, in particular, the relaxation of their spin. In this joint experimental and theoretical analysis, particular focus is put on the crossover between the resonant regime [single-electron tunneling] and the off-resonant regime [inelastic electron (co)tunneling spectroscopy (IETS)]. We show that the interplay of these two processes leads to unexpected mirages of resonances not captured by either of the two pictures alone. Although this turns out to be important in a large fraction of the possible regimes of level positions and bias voltages, it has been given little attention in molecular transport studies. Combined with nonequilibrium IETS—four-electron pump-probe excitations—these mirages provide crucial information on the relaxation of spin excitations. Our encompassing physical picture is supported by a master-equation approach that goes beyond weak coupling. The present work encourages the development of a broader connection between the fields of molecular quantum-dot and scanning probe spectroscopy.

Flickering Quasar Helps Chandra Measure the Expansion Rate of the universe

NASA Astrophysics Data System (ADS)

2000-11-01

Astronomers using the Chandra X-ray Observatory have identified a flickering, four-way mirage image of a distant quasar. A carefully planned observation of this mirage may be used to determine the expansion rate of the universe as well as to measure the distances to extragalactic objects, arguably two of the most important pursuits in modern astronomy. quasar RX J0911.4+0551 This figure is a composite of the X-ray image of the gravitational lens RX J0911.4+551 (top panel) and the light curves of the lensed images A2 (left panel) and A1 (right panel). Credit: NASA George Chartas, senior research associate at The Pennsylvania State University (Penn State) and Marshall W. Bautz, principal research scientist at the Massachusetts Institute of Technology (MIT) Center for Space Research, present their findings today at the meeting of the High Energy Astrophysics Division of the American Astronomical Society in Honolulu, Hawaii. "With a carefully planned follow-up, the Chandra observation of quasar RX J0911.4+0551 may lead to a measurement of the Hubble constant, the expansion rate of the universe, in less than a day," said Chartas. The observation would be done not with mirrors but with mirages--four images of a single quasar that capture the quasar's light at different moments of time due to the speed of light and the location of the mirages. Quasars are extremely distant galaxies with cores that glow with the intensity of 10 trillion Suns, a phenomenon likely powered by a supermassive black hole in the heart of the galaxy. This single "point source" image of a quasar may appear as four or five sources when the quasar--from our vantage point on Earth--is behind a massive intervening deflector, such as a dim galaxy. A mirage of images form when the gravity of the intervening deflector forces light rays to bend and take different paths to reach us. The time it takes for light to reach us from the distant object will depend on which path a ray decides to take. "An intervening galaxy can act as a lens," said Bautz. "Now imagine that the distant lensed quasar suddenly became brighter. The mirage images of the quasar will brighten up at different times depending on the difference in the light travel delay." Unlike ordinary galaxies, quasars do vary greatly in their intensity, especially in the X-ray waveband, said Gordon Garmire, Evan Pugh Professor of Astronomy and Astrophysics at Penn State. This is caused by the violent and erratic flow of gas into the black hole that is powering the quasar. In quasar RX J0911.4+0551, the astronomers saw a sudden brightening of X-ray intensity that lasted for about 2,000 seconds. This was observed in one of the four mirage images. Measuring the time-delay of the 2,000-second flare--or any flare-- from mirage to mirage can provide the absolute distance to the deflector (intervening galaxy) and can thus be used to estimate the expansion rate of the universe. Sjur Refsdal first proposed this promising method in 1964. The method avoids many uncertainties associated with the classic distance-ladder technique used to measure objects and the Hubble constant. The main difficulty in measuring time-delays is that the brightness of each image has to be carefully monitored over several periods of the time-delay. Also, the quasar has to show sufficient variability over time scales smaller than the time-delay. Most attempts to measure time-delays until now have been made in the optical and radio bands. The modest variability of quasars in these wavebands, however, has made it extremely difficult to place accurate constraints on time-delays. X-ray observations of gravitationally lensed quasars, on the other hand, show strong variability over time scales of hours to days. For example, it has taken almost 20 years of optical and radio monitoring to obtain a universal accepted time-delay for the lensed quasar Q0957+561 to an accuracy of 3percent. Chandra has the potential, the team has found, to determine the time-delay in one observation. "Based on computer models developed at Penn State and MIT, we have identified about ten gravitational lens systems with time-delays of less than a day," said Chartas. "One long observation of each source with a superior X-ray telescope could provide enough data to nail down the Hubble constant in the blink of an eye." The team is planning to apply the gravitational-lens method in the near future to several of these systems using the Chandra and XMM-Newton X-ray observatories. The Chandra observations of quasar RX J0911.4+0551 were made on November 2, 1999, using the Advanced CCD Imaging Spectrometer (ACIS). The effort involved several scientists from Penn State and MIT. ACIS was conceived and developed for NASA by Penn State and MIT under Garmire's leadership. NASA's Marshall Space Flight Center in Huntsville, Alabama, manages the Chandra program. TRW, Inc., in Redondo Beach, California, is the prime contractor for the spacecraft. The Smithsonian's Chandra X-ray Center controls science and flight operations from Cambridge, Massachusetts. RX J0911.4+551 Handout Constellation Hydra To follow Chandra's progress, visit the Chandra site at: http://chandra.harvard.edu AND http://chandra.nasa.gov

Refraction in Exoplanet Transit Observations

NASA Astrophysics Data System (ADS)

Dalba, Paul

2018-01-01

Before an exoplanet transit, atmospheric refraction bends light into the line of sight of an observer. The refracted light forms a stellar mirage---a distorted secondary image of the host star---that causes flux increases before transit ingress and after transit egress. The extent of this flux increase provides clues as to the composition and structure of the exoplanetary atmosphere. Here, I model the stellar mirages produced by a comprehensive set of stellar, orbital, planetary, and atmospheric parameters. Refracted light offers unprecedented atmospheric characterization opportunities for cold, long-period gas giant exoplanets. At visible wavelengths, opacity from Rayleigh scattering presents a substantial challenge to detecting stellar mirages for most exoplanets with orbital distances less than 6 AU. Based on physical parameters, I derive a criterion that determines if refracted light will significantly influence observations of a specific exoplanetary system with application to the high-precision Kepler data set. I also investigate the potential for refracted light to identify non-transiting exoplanets and serve as a novel means of out-of-transit atmospheric characterization. The atmospheric lensing events produced by non-transiting exoplanets are more detectable than the corresponding flux increases for transiting exoplanets. Compared to visible light observations, those at red to near-infrared wavelengths are more likely to detect refracted light in an exoplanet atmosphere. With upcoming exoplanet discovery and characterization missions in mind, I consider science cases that are uniquely enabled by photometric and spectroscopic observations of refracted light in exoplanetary systems.

ED03-0078-5

NASA Image and Video Library

2003-03-24

The Altair, a civil variant of the QM-9 Predator B unmanned aerial vehicle (UAV), shows off its lengthy high-aspect ratio wing while on the ramp at General Atomics Aeronautical Systems' flight test facility at El Mirage, California.

Characteristics of the NO-NO2-O3 system in different chemical regimes during the MIRAGE-Mex field campaign

NASA Astrophysics Data System (ADS)

Shon, Z.-H.; Madronich, S.; Song, S.-K.; Flocke, F. M.; Knapp, D. J.; Anderson, R. S.; Shetter, R. E.; Cantrell, C. A.; Hall, S. R.; Tie, X.

2008-12-01

The NO-NO2 system was analyzed in different chemical regimes/air masses based on observations of reactive nitrogen species and peroxy radicals made during the intensive field campaign MIRAGE-Mex (4 to 29 March 2006). The air masses were categorized into 5 groups based on combinations of macroscopic observations, geographical location, meteorological parameters, models, and observations of trace gases: boundary layer (labeled as "BL"), biomass burning ("BB"), free troposphere (continental, "FTCO" and marine, "FTMA"), and Tula industrial complex ("TIC"). In general, NO2/NO ratios in different air masses are near photostationary state. Analysis of this ratio can be useful for testing current understanding of tropospheric chemistry. The ozone production efficiency (OPE) for the 5 air mass categories ranged from 4.5 (TIC) to 8.5 (FTMA), consistent with photochemical aging of air masses exiting the Mexico City Metropolitan Area.

Notes on Experiments.

ERIC Educational Resources Information Center

Physics Education, 1983

1983-01-01

Discusses investigations of mirages with an astronomical telescope and a way of demonstrating three of the main features of laser/maser action. Also discusses several physics demonstrations using color television. These include thin-film interference effects, single-slit diffraction, emission/absorption spectra, "rings and brushes"…

Space Industrialization: The Mirage of Abundance.

ERIC Educational Resources Information Center

Deudney, Daniel

1982-01-01

Large-scale space industrialization is not a viable solution to the population, energy, and resource problems of earth. The expense and technological difficulties involved in the development and maintenance of space manufacturing facilities, space colonies, and large-scale satellites for solar power are discussed. (AM)

Superparticle phenomenology from the natural mini-landscape

NASA Astrophysics Data System (ADS)

Baer, Howard; Barger, Vernon; Savoy, Michael; Serce, Hasan; Tata, Xerxes

2017-06-01

The methodology of the heterotic mini-landscape attempts to zero in on phenomenologically viable corners of the string landscape where the effective low energy theory is the Minimal Supersymmetric Standard Model with localized grand unification. The gaugino mass pattern is that of mirage-mediation. The magnitudes of various SM Yukawa couplings point to a picture where scalar soft SUSY breaking terms are related to the geography of fields in the compactified dimensions. Higgs fields and third generation scalars extend to the bulk and occur in split multiplets with TeV scale soft masses. First and second generation scalars, localized at orbifold fixed points or tori with enhanced symmetry, occur in complete GUT multiplets and have much larger masses. This picture can be matched onto the parameter space of generalized mirage mediation. Naturalness considerations, the requirement of the observed electroweak symmetry breaking pattern, and LHC bounds on m g together limit the gravitino mass to the m 3/2 ˜ 5-60 TeV range. The mirage unification scale is bounded from below with the limit depending on the ratio of squark to gravitino masses. We show that while natural SUSY in this realization may escape detection even at the high luminosity LHC, the high energy LHC with √{s}=33 TeV could unequivocally confirm or exclude this scenario. It should be possible to detect the expected light higgsinos at the ILC if these are kinematically accessible, and possibly also discriminate the expected compression of gaugino masses in the natural mini-landscape picture from the mass pattern expected in models with gaugino mass unification. The thermal WIMP signal should be accessible via direct detection searches at the multi-ton noble liquid detectors such as XENONnT or LZ.

A novel SAMD9 mutation causing MIRAGE syndrome: An expansion and review of phenotype, dysmorphology, and natural history.

PubMed

Jeffries, Lauren; Shima, Hirohito; Ji, Weizhen; Panisello-Manterola, David; McGrath, James; Bird, Lynne M; Konstantino, Monica; Narumi, Satoshi; Lakhani, Saquib

2018-02-01

Germline gain-of-function variants in SAMD9 have been associated with a high risk of mortality and a newly recognized constellation of symptoms described by the acronym MIRAGE: Myelodysplasia, Infection, Restriction of growth, Adrenal insufficiency, Genital phenotypes, and Enteropathy. Here, we describe two additional patients currently living with the syndrome, including one patient with a novel de novo variant for which we provide functional data supporting its pathogenicity. We discuss features of dysmorphology, contrasting with previously described patients as well as drawing attention to additional clinical features, dysautonomia and hearing loss that have not previously been reported. We detail both patients' courses following diagnosis, with attention to treatment plans and recommended specialist care. Our patients are the oldest known with arginine-substituting amino acid variants, and we conclude that early diagnosis and multidisciplinary management may positively impact outcomes for this vulnerable group of patients. © 2017 Wiley Periodicals, Inc.

Research Says/Does Teacher Collaboration Promote Teacher Growth?

ERIC Educational Resources Information Center

Goodwin, Bryan

2016-01-01

A report from TNTP (formerly The New Teacher Project) raised eyebrows recently when it concluded that much of the professional development teachers receive does little to improve teaching quality. The report, provocatively titled "The Mirage: Confronting the Hard Truth About Our Quest for Professional Development," examined the…

Art Education Today: Neither Millennium nor Mirage.

ERIC Educational Resources Information Center

Eisner, Elliot W.

1997-01-01

Reprints the 1966 article as a representative example of thinking about art education during the 1960s. Primarily answers criticisms raised by Victor D'Amico in his attack on the current state of art education, and art education research in particular. Defends this research against charges of irrelevancy and academic indulgence. (MJP)

From Oasis to Mirage: The Aquifers That Won't Replenish.

ERIC Educational Resources Information Center

Gardner, Gary

1995-01-01

Tells the story of three fossil aquifers, in Saudi Arabia, Libya, and the United States, that are mined at nonrenewable rates for agricultural irrigation. Examines the consequences of a collision between rising consumption and falling groundwater supplies. Charts Libya's projected water needs compared to renewable supply, 1985-2030. (LZ)

Educational Charter Schools: A Civil Rights Mirage?

ERIC Educational Resources Information Center

Frankenberg, Erica

2011-01-01

The idea of charter schools arose as a means to allow for innovation by creating schools that were free from traditional regulations, but were held accountable for their performance. More recently, however, charter school advocates have suggested that increasing school choice options will create competition that improves the quality of education…

Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.

PubMed

Watson, Richard A; Mills, Rob; Buckley, C L; Kouvaris, Kostas; Jackson, Adam; Powers, Simon T; Cox, Chris; Tudge, Simon; Davies, Adam; Kounios, Loizos; Power, Daniel

2016-01-01

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term "evolutionary connectionism" to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.

The scope and strength of sex-specific selection in genome evolution.

PubMed

Wright, A E; Mank, J E

2013-09-01

Males and females share the vast majority of their genomes and yet are often subject to different, even conflicting, selection. Genomic and transcriptomic developments have made it possible to assess sex-specific selection at the molecular level, and it is clear that sex-specific selection shapes the evolutionary properties of several genomic characteristics, including transcription, post-transcriptional regulation, imprinting, genome structure and gene sequence. Sex-specific selection is strongly influenced by mating system, which also causes neutral evolutionary changes that affect different regions of the genome in different ways. Here, we synthesize theoretical and molecular work in order to provide a cohesive view of the role of sex-specific selection and mating system in genome evolution. We also highlight the need for a combined approach, incorporating both genomic data and experimental phenotypic studies, in order to understand precisely how sex-specific selection drives evolutionary change across the genome. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Evolutionary inevitability of sexual antagonism.

PubMed

Connallon, Tim; Clark, Andrew G

2014-02-07

Sexual antagonism, whereby mutations are favourable in one sex and disfavourable in the other, is common in natural populations, yet the root causes of sexual antagonism are rarely considered in evolutionary theories of adaptation. Here, we explore the evolutionary consequences of sex-differential selection and genotype-by-sex interactions for adaptation in species with separate sexes. We show that sexual antagonism emerges naturally from sex differences in the direction of selection on phenotypes expressed by both sexes or from sex-by-genotype interactions affecting the expression of such phenotypes. Moreover, modest sex differences in selection or genotype-by-sex effects profoundly influence the long-term evolutionary trajectories of populations with separate sexes, as these conditions trigger the evolution of strong sexual antagonism as a by-product of adaptively driven evolutionary change. The theory demonstrates that sexual antagonism is an inescapable by-product of adaptation in species with separate sexes, whether or not selection favours evolutionary divergence between males and females.

Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals.

PubMed

Huang, Bing-Hong; Liao, Pei-Chun

2015-07-01

Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Time-bound promotions in Indian medical institutes: a mirage?

PubMed

Sukhlecha, Anupama

2016-01-01

Incentives, pay hikes and timely promotions enhance the job performance of an employee. In medical institutes, too, satisfied teachers would train students in a better way leading to better equipped doctors and ultimately, greater patient satisfaction. A study in Malaysia links high levels of satisfaction of employees with good salary, promotions, and incentives.

Fatigue Assessment in Camp Mirage CC130 Aircrew: Recommendations for Pharmacologic Intervention

DTIC Science & Technology

2004-02-20

naturally occurring hormone synthesized by the pineal gland from the precursor amino acid tryptophan (4). In pharmacologic doses, melatonin has a large...the intake of melatonin or placebo. Adv Pineal Res 1991; 5: 303-09. 10. Pang SF, Pang CS, Poon AM, Lee PP, Liu ZM, Shiu SY. Melatonin: a chemical

Grand Illusions: How the Universe Plays Tricks on Us.

ERIC Educational Resources Information Center

Chernin, A. D.

1992-01-01

Presents basic facts about quasars as most powerful sources of radiation in the universe. Describes in detail the mirages and illusions that quasars generate and methods for their interpretation. Includes the notion of the gravitational lens and its relationship to twin quasars and the apparent measure of a quasar's bright jet tail moving faster…

The mirage effect to probe the adsorption of organic molecules on the surface of the mass standards

NASA Astrophysics Data System (ADS)

Taillade, F.; Silva, M. Z.; Lepoutre, F.; Lecollinet, M.; Pinot, P.

2000-05-01

Among all the basic SI units, the mass unit is the only one to be defined in terms of a material standard: a prototype called K. All the industrial countries possess their own standards which were compared to the K during the last international comparison showing that unknown evolution occurs, but the adsorption-desorption of cleaning products plays a relatively important role. A few years ago, several laboratories in the U.S.A., Germany, and France reported interesting results of photothermal measurements to detect desorption at normal temperature and pressure (NTP). This paper presents a mirage set-up built to detect the film of condensable gasses on metallic surfaces at NTP conditions. In order to quantify these measurements, an inverse method has been developed to determine the adsorption isotherm involved in the physical process of adsorption-desorption and the linked parameters such as absorbability, type of adsorption, and differential heat of adsorption. The results will be discussed to imagine possible tracks to reduce the instabilities of the standards in the future and for possible new definitions of standards built with silicon.

Chasing the Mirage: a grounded theory of the clinical reasoning processes that Registered Nurses use to recognize delirium.

PubMed

El Hussein, Mohamed; Hirst, Sandra

2016-02-01

The aim of this study was to construct a grounded theory that explains the clinical reasoning processes that registered nurses use to recognize delirium in older adults in acute care hospitals. Delirium is under-recognized in acute hospital settings, this may stem from underdeveloped clinical reasoning processes. Little is known about registered nurses' (RNs) clinical reasoning processes in complex situations such as delirium recognition. A grounded theory approach was used to analyse interview data about the clinical reasoning processes of RNs in acute hospital settings. Seventeen RNs were recruited. Concurrent data collection and comparative analysis and theoretical sampling were conducted in 2013-2014. The core category to emerge from the data was 'chasing the mirage', which describes RNs' clinical reasoning processes to recognize delirium during their interaction with older adults. Understanding the reasoning that contributes to delirium under-recognition provides a strategy by which, this problem can be brought to the forefront of RNs' awareness and intervention. Delirium recognition will contribute to quality care for older adults. © 2015 John Wiley & Sons Ltd.

The locus of sexual selection: moving sexual selection studies into the post-genomics era.

PubMed

Wilkinson, G S; Breden, F; Mank, J E; Ritchie, M G; Higginson, A D; Radwan, J; Jaquiery, J; Salzburger, W; Arriero, E; Barribeau, S M; Phillips, P C; Renn, S C P; Rowe, L

2015-04-01

Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Evolutionary molecular medicine.

PubMed

Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

2012-05-01

Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

PubMed Central

Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

2015-01-01

Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

Natural selection. IV. The Price equation.

PubMed

Frank, S A

2012-06-01

The Price equation partitions total evolutionary change into two components. The first component provides an abstract expression of natural selection. The second component subsumes all other evolutionary processes, including changes during transmission. The natural selection component is often used in applications. Those applications attract widespread interest for their simplicity of expression and ease of interpretation. Those same applications attract widespread criticism by dropping the second component of evolutionary change and by leaving unspecified the detailed assumptions needed for a complete study of dynamics. Controversies over approximation and dynamics have nothing to do with the Price equation itself, which is simply a mathematical equivalence relation for total evolutionary change expressed in an alternative form. Disagreements about approach have to do with the tension between the relative valuation of abstract versus concrete analyses. The Price equation's greatest value has been on the abstract side, particularly the invariance relations that illuminate the understanding of natural selection. Those abstract insights lay the foundation for applications in terms of kin selection, information theory interpretations of natural selection and partitions of causes by path analysis. I discuss recent critiques of the Price equation by Nowak and van Veelen. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes.

PubMed

Shepelin, Denis; Hansen, Anne Sofie Lærke; Lennen, Rebecca; Luo, Hao; Herrgård, Markus J

2018-05-11

Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering. In evolutionary engineering, in vivo selections for a desired phenotype are combined with either generation of spontaneous mutations or some form of targeted or random mutagenesis. Evolutionary engineering has been used to successfully engineer easily selectable phenotypes, such as utilization of a suboptimal nutrient source or tolerance to inhibitory substrates or products. In this review, we focus primarily on a more challenging problem-the use of evolutionary engineering for improving the production of chemicals in microbes directly. We describe recent developments in evolutionary engineering strategies, in general, and discuss, in detail, case studies where production of a chemical has been successfully achieved through evolutionary engineering by coupling production to cellular growth.

Simulating natural selection in landscape genetics

Treesearch

E. L. Landguth; S. A. Cushman; N. Johnson

2012-01-01

Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially- explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal...

The role of selection on evolutionary rescue

NASA Astrophysics Data System (ADS)

Amirjanov, Adil

The paper investigates the role of selection on evolutionary rescue of population. The statistical mechanics technique is used to model dynamics of a population experiencing a natural selection and an abrupt change in the environment. The paper assesses the selective pressure produced by two different mechanisms: by strength of resistance and by strength of selection (by intraspecific competition). It is shown that both mechanisms are capable of providing an evolutionary rescue of population in particular conditions. However, for a small level of an extinction rate, the population cannot be rescued without intraspecific competition.

Mapping a Mirage: Documenting the Scholarship of Teaching and Learning

ERIC Educational Resources Information Center

Simmons, Nicola

2008-01-01

The purpose of the conference session upon which this paper is based was to challenge the notion that evidence of scholarship must be limited to publication in a peer-reviewed journal, and to open the doors for creative thinking about what might constitute evidence of scholarship of teaching and learning. Existing theory around defining…

Mirages in the Desert: Theorizing Western Muslim Identity across 60 Years

ERIC Educational Resources Information Center

El-Sherif, Lucy

2016-01-01

Theorizations on Western Muslim identity that are multi-layered and grounded in actual Western Muslim experiences are hard to find. Two exceptions to this are "The Road to Mecca" by Muhammad Asad (1954/2005), and "Islam is a Foreign Country" by Zareena Grewal (2014), rich texts that span across six decades. Asad's classic…

[Charles Darwin and the problem of evolutionary progress].

PubMed

Iordanskiĭ, N N

2010-01-01

According to Ch. Darwin's evolutionary theory, evolutionary progress (interpreted as morpho-physiological progress or arogenesis in recent terminology) is one of logical results of natural selection. At the same time, natural selection does not hold any factors especially promoting evolutionary progress. Darwin emphasized that the pattern of evolutionary changes depends on organism nature more than on the pattern of environment changes. Arogenesis specificity is determined by organization of rigorous biological systems - integral organisms. Onward progressive development is determined by fundamental features of living organisms: metabolism and homeostasis. The concept of social Darwinism differs fundamentally from Darwin's ideas about the most important role of social instincts in progress of mankind. Competition and selection play secondary role in socio-cultural progress of human society.

Using Evolutionary Theory to Guide Mental Health Research.

PubMed

Durisko, Zachary; Mulsant, Benoit H; McKenzie, Kwame; Andrews, Paul W

2016-03-01

Evolutionary approaches to medicine can shed light on the origins and etiology of disease. Such an approach may be especially useful in psychiatry, which frequently addresses conditions with heterogeneous presentation and unknown causes. We review several previous applications of evolutionary theory that highlight the ways in which psychiatric conditions may persist despite and because of natural selection. One lesson from the evolutionary approach is that some conditions currently classified as disorders (because they cause distress and impairment) may actually be caused by functioning adaptations operating "normally" (as designed by natural selection). Such conditions suggest an alternative illness model that may generate alternative intervention strategies. Thus, the evolutionary approach suggests that psychiatry should sometimes think differently about distress and impairment. The complexity of the human brain, including normal functioning and potential for dysfunctions, has developed over evolutionary time and has been shaped by natural selection. Understanding the evolutionary origins of psychiatric conditions is therefore a crucial component to a complete understanding of etiology. © The Author(s) 2016.

Using Evolutionary Theory to Guide Mental Health Research

PubMed Central

Mulsant, Benoit H.; McKenzie, Kwame; Andrews, Paul W.

2016-01-01

Evolutionary approaches to medicine can shed light on the origins and etiology of disease. Such an approach may be especially useful in psychiatry, which frequently addresses conditions with heterogeneous presentation and unknown causes. We review several previous applications of evolutionary theory that highlight the ways in which psychiatric conditions may persist despite and because of natural selection. One lesson from the evolutionary approach is that some conditions currently classified as disorders (because they cause distress and impairment) may actually be caused by functioning adaptations operating “normally” (as designed by natural selection). Such conditions suggest an alternative illness model that may generate alternative intervention strategies. Thus, the evolutionary approach suggests that psychiatry should sometimes think differently about distress and impairment. The complexity of the human brain, including normal functioning and potential for dysfunctions, has developed over evolutionary time and has been shaped by natural selection. Understanding the evolutionary origins of psychiatric conditions is therefore a crucial component to a complete understanding of etiology. PMID:27254091

How much can history constrain adaptive evolution? A real-time evolutionary approach of inversion polymorphisms in Drosophila subobscura.

PubMed

Fragata, I; Lopes-Cunha, M; Bárbaro, M; Kellen, B; Lima, M; Santos, M A; Faria, G S; Santos, M; Matos, M; Simões, P

2014-12-01

Chromosomal inversions are present in a wide range of animals and plants, having an important role in adaptation and speciation. Although empirical evidence of their adaptive value is abundant, the role of different processes underlying evolution of chromosomal polymorphisms is not fully understood. History and selection are likely to shape inversion polymorphism variation to an extent yet largely unknown. Here, we perform a real-time evolution study addressing the role of historical constraints and selection in the evolution of these polymorphisms. We founded laboratory populations of Drosophila subobscura derived from three locations along the European cline and followed the evolutionary dynamics of inversion polymorphisms throughout the first 40 generations. At the beginning, populations were highly differentiated and remained so throughout generations. We report evidence of positive selection for some inversions, variable between foundations. Signs of negative selection were more frequent, in particular for most cold-climate standard inversions across the three foundations. We found that previously observed convergence at the phenotypic level in these populations was not associated with convergence in inversion frequencies. In conclusion, our study shows that selection has shaped the evolutionary dynamics of inversion frequencies, but doing so within the constraints imposed by previous history. Both history and selection are therefore fundamental to predict the evolutionary potential of different populations to respond to global environmental changes. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Signatures of selection acting on the innate immunity gene Toll-like receptor 2 (TLR2) during the evolutionary history of rodents.

PubMed

Tschirren, B; Råberg, L; Westerdahl, H

2011-06-01

Patterns of selection acting on immune defence genes have recently been the focus of considerable interest. Yet, when it comes to vertebrates, studies have mainly focused on the acquired branch of the immune system. Consequently, the direction and strength of selection acting on genes of the vertebrate innate immune defence remain poorly understood. Here, we present a molecular analysis of selection on an important receptor of the innate immune system of vertebrates, the Toll-like receptor 2 (TLR2), across 17 rodent species. Although purifying selection was the prevalent evolutionary force acting on most parts of the rodent TLR2, we found that codons in close proximity to pathogen-binding and TLR2-TLR1 heterodimerization sites have been subject to positive selection. This indicates that parasite-mediated selection is not restricted to acquired immune system genes like the major histocompatibility complex, but also affects innate defence genes. To obtain a comprehensive understanding of evolutionary processes in host-parasite systems, both innate and acquired immunity thus need to be considered. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Testing for a genetic response to sexual selection in a wild Drosophila population.

PubMed

Gosden, T P; Thomson, J R; Blows, M W; Schaul, A; Chenoweth, S F

2016-06-01

In accordance with the consensus that sexual selection is responsible for the rapid evolution of display traits on macroevolutionary scales, microevolutionary studies suggest sexual selection is a widespread and often strong form of directional selection in nature. However, empirical evidence for the contemporary evolution of sexually selected traits via sexual rather than natural selection remains weak. In this study, we used a novel application of quantitative genetic breeding designs to test for a genetic response to sexual selection on eight chemical display traits from a field population of the fly, Drosophila serrata. Using our quantitative genetic approach, we were able to detect a genetically based difference in means between groups of males descended from fathers who had either successfully sired offspring or were randomly collected from the same wild population for one of these display traits, the diene (Z,Z)-5,9-C27 : 2 . Our experimental results, in combination with previous laboratory studies on this system, suggest that both natural and sexual selection may be influencing the evolutionary trajectories of these traits in nature, limiting the capacity for a contemporary evolutionary response. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme

PubMed Central

Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

2015-01-01

Molecular biologists have long recognized carcinogenesis as an evolutionary process that involves natural selection. Cancer is driven by the somatic evolution of cell lineages. In this study, the evolution of somatic cancer cell lineages during carcinogenesis was modeled as an equilibrium point (ie, phenotype of attractor) shifting, the process of a nonlinear stochastic evolutionary biological network. This process is subject to intrinsic random fluctuations because of somatic genetic and epigenetic variations, as well as extrinsic disturbances because of carcinogens and stressors. In order to maintain the normal function (ie, phenotype) of an evolutionary biological network subjected to random intrinsic fluctuations and extrinsic disturbances, a network robustness scheme that incorporates natural selection needs to be developed. This can be accomplished by selecting certain genetic and epigenetic variations to modify the network structure to attenuate intrinsic fluctuations efficiently and to resist extrinsic disturbances in order to maintain the phenotype of the evolutionary biological network at an equilibrium point (attractor). However, during carcinogenesis, the remaining (or neutral) genetic and epigenetic variations accumulate, and the extrinsic disturbances become too large to maintain the normal phenotype at the desired equilibrium point for the nonlinear evolutionary biological network. Thus, the network is shifted to a cancer phenotype at a new equilibrium point that begins a new evolutionary process. In this study, the natural selection scheme of an evolutionary biological network of carcinogenesis was derived from a robust negative feedback scheme based on the nonlinear stochastic Nash game strategy. The evolvability and phenotypic robustness criteria of the evolutionary cancer network were also estimated by solving a Hamilton–Jacobi inequality – constrained optimization problem. The simulation revealed that the phenotypic shift of the lung cancer-associated cell network takes 54.5 years from a normal state to stage I cancer, 1.5 years from stage I to stage II cancer, and 2.5 years from stage II to stage III cancer, with a reasonable match for the statistical result of the average age of lung cancer. These results suggest that a robust negative feedback scheme, based on a stochastic evolutionary game strategy, plays a critical role in an evolutionary biological network of carcinogenesis under a natural selection scheme. PMID:26244004

Is the Allure of Self-Esteem a Mirage after All?

ERIC Educational Resources Information Center

Krueger, Joachim I.; Vohs, Kathleen D.; Baumeister, Roy F.

2008-01-01

Comments on the original article "Do people's self-views matter? Self-concept and self-esteem in everyday life," by W. B. Swann, Jr., C. Chang-Schneider, and K. L. McClarty (2007). Swann et al argued that people's self-views, and their global self-esteem in particular, yield a suite of behavioral effects that are beneficial to the individual and…

Phenomenology of NMSSM in TeV scale mirage mediation

NASA Astrophysics Data System (ADS)

Hagimoto, Kei; Kobayashi, Tatsuo; Makino, Hiroki; Okumura, Ken-ichi; Shimomura, Takashi

2016-02-01

We study the next-to-minimal supersymmetric standard model (NMSSM) with the TeV scale mirage mediation, which is known as a solution for the little hierarchy problem in supersymmetry. Our previous study showed that 125 GeV Higgs boson is realized with {O} (10)% fine-tuning for 1.5 TeV gluino (1 TeV stop) mass. The μ term could be as large as 500 GeV without sacrificing the fine-tuning thanks to a cancellation mechanism. The singlet-doublet mixing is suppressed by tan β. In this paper, we further extend this analysis. We argue that approximate scale symmetries play a role behind the suppression of the singlet-doublet mixing. They reduce the mixing matrix to a simple form that is useful to understand the results of the numerical analysis. We perform a comprehensive analysis of the fine-tuning including the singlet sector by introducing a simple formula for the fine-tuning measure. This shows that the singlet mass of the least fine-tuning is favored by the LEP anomaly for moderate tan β. We also discuss prospects for the precision measurements of the Higgs couplings at LHC and ILC and direct/indirect dark matter searches in the model.

Why don't zebras have machine guns? Adaptation, selection, and constraints in evolutionary theory.

PubMed

Shanahan, Timothy

2008-03-01

In an influential paper, Stephen Jay Gould and Richard Lewontin (1979) contrasted selection-driven adaptation with phylogenetic, architectural, and developmental constraints as distinct causes of phenotypic evolution. In subsequent publications Gould (e.g., 1997a,b, 2002) has elaborated this distinction into one between a narrow "Darwinian Fundamentalist" emphasis on "external functionalist" processes, and a more inclusive "pluralist" emphasis on "internal structuralist" principles. Although theoretical integration of functionalist and structuralist explanations is the ultimate aim, natural selection and internal constraints are treated as distinct causes of evolutionary change. This distinction is now routinely taken for granted in the literature in evolutionary biology. I argue that this distinction is problematic because the effects attributed to non-selective constraints are more parsimoniously explained as the ordinary effects of selection itself. Although it may still be a useful shorthand to speak of phylogenetic, architectural, and developmental constraints on phenotypic evolution, it is important to understand that such "constraints" do not constitute an alternative set of causes of evolutionary change. The result of this analysis is a clearer understanding of the relationship between adaptation, selection and constraints as explanatory concepts in evolutionary theory.

Evolutionary rates for multivariate traits: the role of selection and genetic variation

PubMed Central

Pitchers, William; Wolf, Jason B.; Tregenza, Tom; Hunt, John; Dworkin, Ian

2014-01-01

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation (), which predicts evolutionary change for a suite of phenotypic traits () as a product of directional selection acting on them (β) and the genetic variance–covariance matrix for those traits (G). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates. PMID:25002697

The Evolution of Different Forms of Sociality: Behavioral Mechanisms and Eco-Evolutionary Feedback

PubMed Central

van der Post, Daniel J.; Verbrugge, Rineke; Hemelrijk, Charlotte K.

2015-01-01

Different forms of sociality have evolved via unique evolutionary trajectories. However, it remains unknown to what extent trajectories of social evolution depend on the specific characteristics of different species. Our approach to studying such trajectories is to use evolutionary case-studies, so that we can investigate how grouping co-evolves with a multitude of individual characteristics. Here we focus on anti-predator vigilance and foraging. We use an individual-based model, where behavioral mechanisms are specified, and costs and benefits are not predefined. We show that evolutionary changes in grouping alter selection pressures on vigilance, and vice versa. This eco-evolutionary feedback generates an evolutionary progression from “leader-follower” societies to “fission-fusion” societies, where cooperative vigilance in groups is maintained via a balance between within- and between-group selection. Group-level selection is generated from an assortment that arises spontaneously when vigilant and non-vigilant foragers have different grouping tendencies. The evolutionary maintenance of small groups, and cooperative vigilance in those groups, is therefore achieved simultaneously. The evolutionary phases, and the transitions between them, depend strongly on behavioral mechanisms. Thus, integrating behavioral mechanisms and eco-evolutionary feedback is critical for understanding what kinds of intermediate stages are involved during the evolution of particular forms of sociality. PMID:25629313

The evolution of different forms of sociality: behavioral mechanisms and eco-evolutionary feedback.

PubMed

van der Post, Daniel J; Verbrugge, Rineke; Hemelrijk, Charlotte K

2015-01-01

Different forms of sociality have evolved via unique evolutionary trajectories. However, it remains unknown to what extent trajectories of social evolution depend on the specific characteristics of different species. Our approach to studying such trajectories is to use evolutionary case-studies, so that we can investigate how grouping co-evolves with a multitude of individual characteristics. Here we focus on anti-predator vigilance and foraging. We use an individual-based model, where behavioral mechanisms are specified, and costs and benefits are not predefined. We show that evolutionary changes in grouping alter selection pressures on vigilance, and vice versa. This eco-evolutionary feedback generates an evolutionary progression from "leader-follower" societies to "fission-fusion" societies, where cooperative vigilance in groups is maintained via a balance between within- and between-group selection. Group-level selection is generated from an assortment that arises spontaneously when vigilant and non-vigilant foragers have different grouping tendencies. The evolutionary maintenance of small groups, and cooperative vigilance in those groups, is therefore achieved simultaneously. The evolutionary phases, and the transitions between them, depend strongly on behavioral mechanisms. Thus, integrating behavioral mechanisms and eco-evolutionary feedback is critical for understanding what kinds of intermediate stages are involved during the evolution of particular forms of sociality.

Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica.

PubMed

Guo, Yue; Liu, Jing; Zhang, Jiefu; Liu, Shengyi; Du, Jianchang

2017-07-01

It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories: positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (K a ) and the rates of synonymous substitution (K s ) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs. The resulting data show that PSGs have higher protein evolutionary rates, lower synonymous substitution rates, shorter gene length, fewer exons, higher functional specificity, lower expression level, higher tissue-specific expression and stronger codon bias than NSGs. Although the quantities and values are different, the relative features of PSGs and NSGs have been largely verified in the model species Arabidopsis. These data suggest that PSGs and NSGs differ not only under selective pressure (K a /K s ), but also in their evolutionary, structural and functional properties, indicating that selective modes may serve as a determinant factor for measuring evolutionary rates, gene compactness and expression patterns in Brassica. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

An evolutionary perspective on leaf economics: phylogenetics of leaf mass per area in vascular plants

PubMed Central

Flores, Olivier; Garnier, Eric; Wright, Ian J; Reich, Peter B; Pierce, Simon; Dìaz, Sandra; Pakeman, Robin J; Rusch, Graciela M; Bernard-Verdier, Maud; Testi, Baptiste; Bakker, Jan P; Bekker, Renée M; Cerabolini, Bruno E L; Ceriani, Roberta M; Cornu, Guillaume; Cruz, Pablo; Delcamp, Matthieu; Dolezal, Jiri; Eriksson, Ove; Fayolle, Adeline; Freitas, Helena; Golodets, Carly; Gourlet-Fleury, Sylvie; Hodgson, John G; Brusa, Guido; Kleyer, Michael; Kunzmann, Dieter; Lavorel, Sandra; Papanastasis, Vasilios P; Pérez-Harguindeguy, Natalia; Vendramini, Fernanda; Weiher, Evan

2014-01-01

In plant leaves, resource use follows a trade-off between rapid resource capture and conservative storage. This “worldwide leaf economics spectrum” consists of a suite of intercorrelated leaf traits, among which leaf mass per area, LMA, is one of the most fundamental as it indicates the cost of leaf construction and light-interception borne by plants. We conducted a broad-scale analysis of the evolutionary history of LMA across a large dataset of 5401 vascular plant species. The phylogenetic signal in LMA displayed low but significant conservatism, that is, leaf economics tended to be more similar among close relatives than expected by chance alone. Models of trait evolution indicated that LMA evolved under weak stabilizing selection. Moreover, results suggest that different optimal phenotypes evolved among large clades within which extremes tended to be selected against. Conservatism in LMA was strongly related to growth form, as were selection intensity and phenotypic evolutionary rates: woody plants showed higher conservatism in relation to stronger stabilizing selection and lower evolutionary rates compared to herbaceous taxa. The evolutionary history of LMA thus paints different evolutionary trajectories of vascular plant species across clades, revealing the coordination of leaf trait evolution with growth forms in response to varying selection regimes. PMID:25165520

Fitness costs and benefits of novel herbicide tolerance in a noxious weed

PubMed Central

Baucom, Regina S.; Mauricio, Rodney

2004-01-01

Glyphosate, the active ingredient in the herbicide RoundUp, has increased dramatically in use over the past decade and constitutes a potent anthropogenic source of selection. In the southeastern United States, weedy morning glories have begun to develop tolerance to glyphosate, representing a unique opportunity to examine the evolutionary genetics of a novel trait. We found genetic variation for tolerance, indicating the potential for the population to respond to selection by glyphosate. However, the following significant evolutionary constraint exists: in the absence of glyphosate, tolerant genotypes produced fewer seeds than susceptible genotypes. The combination of strong positive directional selection in the presence of glyphosate and strong negative directional selection in its absence may indicate that the selective landscape of land use could drive the evolutionary trajectory of glyphosate tolerance. Understanding these evolutionary forces is imperative for devising comprehensive management strategies to help slow the rate of the evolution of tolerance. PMID:15326309

Evolutionary domestication in Drosophila subobscura.

PubMed

Simões, P; Rose, M R; Duarte, A; Gonçalves, R; Matos, M

2007-03-01

The domestication of plants and animals is historically one of the most important topics in evolutionary biology. The evolutionary genetic changes arising from human cultivation are complex because of the effects of such varied processes as continuing natural selection, artificial selection, deliberate inbreeding, genetic drift and hybridization of different lineages. Despite the interest of domestication as an evolutionary process, few studies of multicellular sexual species have approached this topic using well-replicated experiments. Here we present a comprehensive study in which replicated evolutionary trajectories from several Drosophila subobscura populations provide a detailed view of the evolutionary dynamics of domestication in an outbreeding animal species. Our results show a clear evolutionary response in fecundity traits, but no clear pattern for adult starvation resistance and juvenile traits such as development time and viability. These results supply new perspectives on the confounding of adaptation with other evolutionary mechanisms in the process of domestication.

Determining Selection across Heterogeneous Landscapes: A Perturbation-Based Method and Its Application to Modeling Evolution in Space.

PubMed

Wickman, Jonas; Diehl, Sebastian; Blasius, Bernd; Klausmeier, Christopher A; Ryabov, Alexey B; Brännström, Åke

2017-04-01

Spatial structure can decisively influence the way evolutionary processes unfold. To date, several methods have been used to study evolution in spatial systems, including population genetics, quantitative genetics, moment-closure approximations, and individual-based models. Here we extend the study of spatial evolutionary dynamics to eco-evolutionary models based on reaction-diffusion equations and adaptive dynamics. Specifically, we derive expressions for the strength of directional and stabilizing/disruptive selection that apply both in continuous space and to metacommunities with symmetrical dispersal between patches. For directional selection on a quantitative trait, this yields a way to integrate local directional selection across space and determine whether the trait value will increase or decrease. The robustness of this prediction is validated against quantitative genetics. For stabilizing/disruptive selection, we show that spatial heterogeneity always contributes to disruptive selection and hence always promotes evolutionary branching. The expression for directional selection is numerically very efficient and hence lends itself to simulation studies of evolutionary community assembly. We illustrate the application and utility of the expressions for this purpose with two examples of the evolution of resource utilization. Finally, we outline the domain of applicability of reaction-diffusion equations as a modeling framework and discuss their limitations.

How Can We Study the Evolution of Animal Minds?

PubMed Central

Cauchoix, Maxime; Chaine, Alexis S.

2016-01-01

During the last 50 years, comparative cognition and neurosciences have improved our understanding of animal minds while evolutionary ecology has revealed how selection acts on traits through evolutionary time. We describe how cognition can be subject to natural selection like any other biological trait and how this evolutionary approach can be used to understand the evolution of animal cognition. We recount how comparative and fitness methods have been used to understand the evolution of cognition and outline how these approaches could extend our understanding of cognition. The fitness approach, in particular, offers unprecedented opportunities to study the evolutionary mechanisms responsible for variation in cognition within species and could allow us to investigate both proximate (i.e., neural and developmental) and ultimate (i.e., ecological and evolutionary) underpinnings of animal cognition together. We highlight recent studies that have successfully shown that cognitive traits can be under selection, in particular by linking individual variation in cognition to fitness. To bridge the gap between cognitive variation and fitness consequences and to better understand why and how selection can occur on cognition, we end this review by proposing a more integrative approach to study contemporary selection on cognitive traits combining socio-ecological data, minimally invasive neuroscience methods and measurement of ecologically relevant behaviors linked to fitness. Our overall goal in this review is to build a bridge between cognitive neuroscientists and evolutionary biologists, illustrate how their research could be complementary, and encourage evolutionary ecologists to include explicit attention to cognitive processes in their studies of behavior. PMID:27014163

General intelligence is an emerging property, not an evolutionary puzzle.

PubMed

Ramus, Franck

2017-01-01

Burkart et al. contend that general intelligence poses a major evolutionary puzzle. This assertion presupposes a reification of general intelligence - that is, assuming that it is one "thing" that must have been selected as such. However, viewing general intelligence as an emerging property of multiple cognitive abilities (each with their own selective advantage) requires no additional evolutionary explanation.

Evolutionary foundations for cancer biology.

PubMed

Aktipis, C Athena; Nesse, Randolph M

2013-01-01

New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles-cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations-provide a foundation for understanding, preventing, and treating cancer.

Evolutionary foundations for cancer biology

PubMed Central

Aktipis, C Athena; Nesse, Randolph M

2013-01-01

New applications of evolutionary biology are transforming our understanding of cancer. The articles in this special issue provide many specific examples, such as microorganisms inducing cancers, the significance of within-tumor heterogeneity, and the possibility that lower dose chemotherapy may sometimes promote longer survival. Underlying these specific advances is a large-scale transformation, as cancer research incorporates evolutionary methods into its toolkit, and asks new evolutionary questions about why we are vulnerable to cancer. Evolution explains why cancer exists at all, how neoplasms grow, why cancer is remarkably rare, and why it occurs despite powerful cancer suppression mechanisms. Cancer exists because of somatic selection; mutations in somatic cells result in some dividing faster than others, in some cases generating neoplasms. Neoplasms grow, or do not, in complex cellular ecosystems. Cancer is relatively rare because of natural selection; our genomes were derived disproportionally from individuals with effective mechanisms for suppressing cancer. Cancer occurs nonetheless for the same six evolutionary reasons that explain why we remain vulnerable to other diseases. These four principles—cancers evolve by somatic selection, neoplasms grow in complex ecosystems, natural selection has shaped powerful cancer defenses, and the limitations of those defenses have evolutionary explanations—provide a foundation for understanding, preventing, and treating cancer. PMID:23396885

The Challenges of ICT in Higher Education: The Mirage in ICT Use in Higher Education

ERIC Educational Resources Information Center

Okeiga, N. I. Obi; Okumu-Bigambo, W.; Masibo, P. F. Lumala

2010-01-01

The significance of ICT's influence as the epitome of information cannot be overemphasized. Globalization is multi-directional and interactive in nature masks ICT, and much of its content as a Western orientation and control over communication. The paper sets to show that there are imbalances in the use of ICT in higher education as used in Africa…

An experimental test of density-dependent selection on temperament traits of activity, boldness and sociability.

PubMed

Le Galliard, J-F; Paquet, M; Mugabo, M

2015-05-01

Temperament traits are seen in many animal species, and recent evolutionary models predict that they could be maintained by heterogeneous selection. We tested this prediction by examining density-dependent selection in juvenile common lizards Zootoca vivipara scored for activity, boldness and sociability at birth and at the age of 1 year. We measured three key life-history traits (juvenile survival, body growth rate and reproduction) and quantified selection in experimental populations at five density levels ranging from low to high values. We observed consistent individual differences for all behaviours on the short term, but only for activity and one boldness measure across the first year of life. At low density, growth selection favoured more sociable lizards, whereas viability selection favoured less active individuals. A significant negative correlational selection on activity and boldness existed for body growth rate irrespective of density. Thus, behavioural traits were characterized by limited ontogenic consistency, and natural selection was heterogeneous between density treatments and fitness traits. This confirms that density-dependent selection plays an important role in the maintenance of individual differences in exploration-activity and sociability. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Evolutionary Nephrology.

PubMed

Chevalier, Robert L

2017-05-01

Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.

Disruptive selection as a driver of evolutionary branching and caste evolution in social insects.

PubMed

Planqué, R; Powell, S; Franks, N R; van den Berg, J B

2016-11-01

Theory suggests that evolutionary branching via disruptive selection may be a relatively common and powerful force driving phenotypic divergence. Here, we extend this theory to social insects, which have novel social axes of phenotypic diversification. Our model, built around turtle ant (Cephalotes) biology, is used to explore whether disruptive selection can drive the evolutionary branching of divergent colony phenotypes that include a novel soldier caste. Soldier evolution is a recurrent theme in social insect diversification that is exemplified in the turtle ants. We show that phenotypic mutants can gain competitive advantages that induce disruptive selection and subsequent branching. A soldier caste does not generally appear before branching, but can evolve from subsequent competition. The soldier caste then evolves in association with specialized resource preferences that maximize defensive performance. Overall, our model indicates that resource specialization may occur in the absence of morphological specialization, but that when morphological specialization evolves, it is always in association with resource specialization. This evolutionary coupling of ecological and morphological specialization is consistent with recent empirical evidence, but contrary to predictions of classical caste theory. Our model provides a new theoretical understanding of the ecology of caste evolution that explicitly considers the process of adaptive phenotypic divergence and diversification. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evolutionary rates for multivariate traits: the role of selection and genetic variation.

PubMed

Pitchers, William; Wolf, Jason B; Tregenza, Tom; Hunt, John; Dworkin, Ian

2014-08-19

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation (Δz(-)=Gβ), which predicts evolutionary change for a suite of phenotypic traits (Δz(-)) as a product of directional selection acting on them (β) and the genetic variance-covariance matrix for those traits (G ). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Sexual selection on female ornaments in the sex-role-reversed Gulf pipefish (Syngnathus scovelli).

PubMed

Flanagan, S P; Johnson, J B; Rose, E; Jones, A G

2014-11-01

Understanding how selection acts on traits individually and in combination is an important step in deciphering the mechanisms driving evolutionary change, but for most species, and especially those in which sexual selection acts more strongly on females than on males, we have no estimates of selection coefficients pertaining to the multivariate sexually selected phenotype. Here, we use a laboratory-based mesocosm experiment to quantify pre- and post-mating selection on female secondary sexual traits in the Gulf pipefish (Syngnathus scovelli), a sexually dimorphic, sex-role-reversed species in which ornamented females compete for access to choosy males. We calculate selection differentials and gradients on female traits, including ornament area, ornament number and body size for three episodes of selection related to female reproductive success (number of mates, number of eggs transferred and number of surviving embryos). Selection is strong on both ornament area and ornament size, and the majority of selection occurs during the premating episode of selection. Interestingly, selection on female body size, which has been detected in previous studies of Gulf pipefish, appears to be indirect, as evidenced by a multivariate analysis of selection gradients. Our results show that sexual selection favours either many bands or larger bands in female Gulf pipefish. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

PubMed

Bonnet, Timothée; Wandeler, Peter; Camenisch, Glauco; Postma, Erik

2017-01-01

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called "stasis paradox" highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is superior to purely phenotypic estimates of selection and evolutionary change.

Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population

PubMed Central

Wandeler, Peter; Camenisch, Glauco

2017-01-01

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is superior to purely phenotypic estimates of selection and evolutionary change. PMID:28125583

The effects of stress and sex on selection, genetic covariance, and the evolutionary response.

PubMed

Holman, L; Jacomb, F

2017-10-01

The capacity of a population to adapt to selection (evolvability) depends on whether the structure of genetic variation permits the evolution of fitter trait combinations. Selection, genetic variance and genetic covariance can change under environmental stress, and males and females are not genetically independent, yet the combined effects of stress and dioecy on evolvability are not well understood. Here, we estimate selection, genetic (co)variance and evolvability in both sexes of Tribolium castaneum flour beetles under stressful and benign conditions, using a half-sib breeding design. Although stress uncovered substantial latent heritability, stress also affected genetic covariance, such that evolvability remained low under stress. Sexual selection on males and natural selection on females favoured a similar phenotype, and there was positive intersex genetic covariance. Consequently, sexual selection on males augmented adaptation in females, and intralocus sexual conflict was weak or absent. This study highlights that increased heritability does not necessarily increase evolvability, suggests that selection can deplete genetic variance for multivariate trait combinations with strong effects on fitness, and tests the recent hypothesis that sexual conflict is weaker in stressful or novel environments. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Why don’t you use Evolutionary Algorithms in Big Data?

NASA Astrophysics Data System (ADS)

Stanovov, Vladimir; Brester, Christina; Kolehmainen, Mikko; Semenkina, Olga

2017-02-01

In this paper we raise the question of using evolutionary algorithms in the area of Big Data processing. We show that evolutionary algorithms provide evident advantages due to their high scalability and flexibility, their ability to solve global optimization problems and optimize several criteria at the same time for feature selection, instance selection and other data reduction problems. In particular, we consider the usage of evolutionary algorithms with all kinds of machine learning tools, such as neural networks and fuzzy systems. All our examples prove that Evolutionary Machine Learning is becoming more and more important in data analysis and we expect to see the further development of this field especially in respect to Big Data.

Fin propulsion on a human-powered submarine

NASA Astrophysics Data System (ADS)

Anderson, Iain A.; Pocock, Benjamin; Harbuz, Antoni; Algie, Cam; Vochezer, Daniel; Chao, Ryan; Lu, Benjamin

2015-03-01

Nearly all surface and underwater vessels are driven by screw propulsion; ideal for coupling to rotary engines and well understood after over a century of development. But most aquatic creatures use fins for swimming. Although there are sound evolutionary reasons why fish have fins and not propellers, they are nevertheless agile, fast and efficient. Although fish-like robots such as the MIT Robotuna are providing good insight into fin-based swimming there are advantages for using humans in the experimental device. Like an airplane test pilot they can write crash reports. We present preliminary observations for the human powered finned submarine: Taniwha. The sub participated in the 2nd European International Submarine races in Gosport UK where it received a trophy for "Best Non-Propeller Performance". Two sets of Hobie Mirage fin drives fixed to the upper and lower rear surfaces of the sub are pedaled by the pilot. The pilot also has two levers at the front, one to pitch a pair of dive planes and one for yawing a large rudder. Good speed, we estimate to be greater than 6 m/s is possible with these fins although we haven't explored their full potential. Straying too near the surface or bottom can lead to an instability, synonymous to a stall, such that control is lost. The mechanism for this will be discussed and solutions offered. Fish are 400 million years in front of us but one day we'll catch them.

Evolutionary games on cycles with strong selection

NASA Astrophysics Data System (ADS)

Altrock, P. M.; Traulsen, A.; Nowak, M. A.

2017-02-01

Evolutionary games on graphs describe how strategic interactions and population structure determine evolutionary success, quantified by the probability that a single mutant takes over a population. Graph structures, compared to the well-mixed case, can act as amplifiers or suppressors of selection by increasing or decreasing the fixation probability of a beneficial mutant. Properties of the associated mean fixation times can be more intricate, especially when selection is strong. The intuition is that fixation of a beneficial mutant happens fast in a dominance game, that fixation takes very long in a coexistence game, and that strong selection eliminates demographic noise. Here we show that these intuitions can be misleading in structured populations. We analyze mean fixation times on the cycle graph under strong frequency-dependent selection for two different microscopic evolutionary update rules (death-birth and birth-death). We establish exact analytical results for fixation times under strong selection and show that there are coexistence games in which fixation occurs in time polynomial in population size. Depending on the underlying game, we observe inherence of demographic noise even under strong selection if the process is driven by random death before selection for birth of an offspring (death-birth update). In contrast, if selection for an offspring occurs before random removal (birth-death update), then strong selection can remove demographic noise almost entirely.

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals

PubMed Central

Sunagar, Kartik; Moran, Yehu

2015-01-01

Animal venoms are theorized to evolve under the significant influence of positive Darwinian selection in a chemical arms race scenario, where the evolution of venom resistance in prey and the invention of potent venom in the secreting animal exert reciprocal selection pressures. Venom research to date has mainly focused on evolutionarily younger lineages, such as snakes and cone snails, while mostly neglecting ancient clades (e.g., cnidarians, coleoids, spiders and centipedes). By examining genome, venom-gland transcriptome and sequences from the public repositories, we report the molecular evolutionary regimes of several centipede and spider toxin families, which surprisingly accumulated low-levels of sequence variations, despite their long evolutionary histories. Molecular evolutionary assessment of over 3500 nucleotide sequences from 85 toxin families spanning the breadth of the animal kingdom has unraveled a contrasting evolutionary strategy employed by ancient and evolutionarily young clades. We show that the venoms of ancient lineages remarkably evolve under the heavy constraints of negative selection, while toxin families in lineages that originated relatively recently rapidly diversify under the influence of positive selection. We propose that animal venoms mostly employ a ‘two-speed’ mode of evolution, where the major influence of diversifying selection accompanies the earlier stages of ecological specialization (e.g., diet and range expansion) in the evolutionary history of the species–the period of expansion, resulting in the rapid diversification of the venom arsenal, followed by longer periods of purifying selection that preserve the potent toxin pharmacopeia–the period of purification and fixation. However, species in the period of purification may re-enter the period of expansion upon experiencing a major shift in ecology or environment. Thus, we highlight for the first time the significant roles of purifying and episodic selections in shaping animal venoms. PMID:26492532

Dysart Unified School District: How One School District Used Collaborative Planning to Improve Outcomes for All Students. From the Field. Digital Learning Series

ERIC Educational Resources Information Center

Slaven, Chip; Hall, Sara; Schwartzbeck, Terri Duggan; Jones, Rachel; Wolf, Mary Ann

2013-01-01

The Dysart Unified School District (Dysart) in Arizona covers 140 square miles and serves numerous communities, including the cities of Surprise and El Mirage and some unincorporated areas of Maricopa County. At one time the fastest-growing school system in Arizona, Dysart has tripled in size since 2000. The district continues to grow, and in…

The Unattainable Mirage of Equality in American Teacher Education Programs: My Experience

ERIC Educational Resources Information Center

Mukuria, Gathogo M.

2010-01-01

I came to this country with an open mind to pursue the American dream. It did not take me a long to recognize racial disparity as a student and even more so when I became a faculty member in various teacher preparation programs. While I try to evade discussion on race, it is inevitable to talk about it because it seems to be the criteria upon…

Galaxies as High-resolution Telescopes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnacka, Anna, E-mail: abarnacka@cfa.harvard.edu

Recent observations show a population of active galaxies with milliarcsecond offsets between optical and radio emission. Such offsets can be an indication of extreme phenomena associated with supermassive black holes including relativistic jets, binary supermassive black holes, or even recoiling supermassive black holes. However, the multi-wavelength structure of active galaxies at a few milliarcseconds cannot be resolved with direct observations. We propose using strong gravitational lensing to elucidate the multi-wavelength structure of sources. When sources are located close to the caustic of a lensing galaxy, even a small offset in the position of the sources results in a drastic differencemore » in the position and magnification of mirage images. We show that the angular offset in the position of the sources can be amplified more than 50 times in the observed position of mirage images. We find that at least 8% of the observed gravitationally lensed quasars will be in the caustic configuration. The synergy between SKA and Euclid will provide an ideal set of observations for thousands of gravitationally lensed sources in the caustic configuration, which will allow us to resolve the multi-wavelength structure for a large ensemble of sources and to study the physical origin of radio emissions, their connection to supermassive black holes, and their cosmic evolution.« less

Mirage effect from thermally modulated transparent carbon nanotube sheets.

PubMed

Aliev, Ali E; Gartstein, Yuri N; Baughman, Ray H

2011-10-28

The single-beam mirage effect, also known as photothermal deflection, is studied using a free-standing, highly aligned carbon nanotube aerogel sheet as the heat source. The extremely low thermal capacitance and high heat transfer ability of these transparent forest-drawn carbon nanotube sheets enables high frequency modulation of sheet temperature over an enormous temperature range, thereby providing a sharp, rapidly changing gradient of refractive index in the surrounding liquid or gas. The advantages of temperature modulation using carbon nanotube sheets are multiple: in inert gases the temperature can reach > 2500 K; the obtained frequency range for photothermal modulation is ~100 kHz in gases and over 100 Hz in high refractive index liquids; and the heat source is transparent for optical and acoustical waves. Unlike for conventional heat sources for photothermal deflection, the intensity and phase of the thermally modulated beam component linearly depends upon the beam-to-sheet separation over a wide range of distances. This aspect enables convenient measurements of accurate values for thermal diffusivity and the temperature dependence of refractive index for both liquids and gases. The remarkable performance of nanotube sheets suggests possible applications as photo-deflectors and for switchable invisibility cloaks, and provides useful insights into their use as thermoacoustic projectors and sonar. Visibility cloaking is demonstrated in a liquid.

Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents.

PubMed

Gilbert, Scott F; Bosch, Thomas C G; Ledón-Rettig, Cristina

2015-10-01

The integration of research from developmental biology and ecology into evolutionary theory has given rise to a relatively new field, ecological evolutionary developmental biology (Eco-Evo-Devo). This field integrates and organizes concepts such as developmental symbiosis, developmental plasticity, genetic accommodation, extragenic inheritance and niche construction. This Review highlights the roles that developmental symbiosis and developmental plasticity have in evolution. Developmental symbiosis can generate particular organs, can produce selectable genetic variation for the entire animal, can provide mechanisms for reproductive isolation, and may have facilitated evolutionary transitions. Developmental plasticity is crucial for generating novel phenotypes, facilitating evolutionary transitions and altered ecosystem dynamics, and promoting adaptive variation through genetic accommodation and niche construction. In emphasizing such non-genomic mechanisms of selectable and heritable variation, Eco-Evo-Devo presents a new layer of evolutionary synthesis.

Differences in the selection response of serially repeated color pattern characters: standing variation, development, and evolution.

PubMed

Allen, Cerisse E; Beldade, Patrícia; Zwaan, Bas J; Brakefield, Paul M

2008-03-26

There is spectacular morphological diversity in nature but lineages typically display a limited range of phenotypes. Because developmental processes generate the phenotypic variation that fuels natural selection, they are a likely source of evolutionary biases, facilitating some changes and limiting others. Although shifts in developmental regulation are associated with morphological differences between taxa, it is unclear how underlying mechanisms affect the rate and direction of evolutionary change within populations under selection. Here we focus on two ecologically relevant features of butterfly wing color patterns, eyespot size and color composition, which are similarly and strongly correlated across the serially repeated eyespots. Though these two characters show similar patterns of standing variation and covariation within a population, they differ in key features of their underlying development. We targeted pairs of eyespots with artificial selection for coordinated (concerted selection) versus independent (antagonistic selection) change in their color composition and size and compared evolutionary responses of the two color pattern characters. The two characters respond to selection in strikingly different ways despite initially similar patterns of variation in all directions present in the starting population. Size (determined by local properties of a diffusing inductive signal) evolves flexibly in all selected directions. However, color composition (determined by a tissue-level response to the signal concentration gradient) evolves only in the direction of coordinated change. There was no independent evolutionary change in the color composition of two eyespots in response to antagonistic selection. Moreover, these differences in the directions of short-term evolutionary change in eyespot size and color composition within a single species are consistent with the observed wing pattern diversity in the genus. Both characters respond rapidly to selection for coordinated change, but there are striking differences in their response to selection for antagonistic, independent change across eyespots. While many additional factors may contribute to both short- and long-term evolutionary response, we argue that the compartmentalization of developmental processes can influence the diversification of serial repeats such as butterfly eyespots, even under strong selection.

Entrepreneurs and Evolutionary Biology: The Relationship between Testosterone and New Venture Creation

ERIC Educational Resources Information Center

White, Roderick E.; Thornhill, Stewart; Hampson, Elizabeth

2006-01-01

Biological evolutionary processes select for heritable behaviors providing a survival and reproductive advantage. Accordingly, how we behave is, at least in part, affected by the evolutionary history of our species. This research uses evolutionary psychology as the theoretical perspective for exploring the relationship between a heritable…

Sexual selection and the evolution of secondary sexual traits: sex comb evolution in Drosophila.

PubMed

Snook, Rhonda R; Gidaszewski, Nelly A; Chapman, Tracey; Simmons, Leigh W

2013-04-01

Sexual selection can drive rapid evolutionary change in reproductive behaviour, morphology and physiology. This often leads to the evolution of sexual dimorphism, and continued exaggerated expression of dimorphic sexual characteristics, although a variety of other alternative selection scenarios exist. Here, we examined the evolutionary significance of a rapidly evolving, sexually dimorphic trait, sex comb tooth number, in two Drosophila species. The presence of the sex comb in both D. melanogaster and D. pseudoobscura is known to be positively related to mating success, although little is yet known about the sexually selected benefits of sex comb structure. In this study, we used experimental evolution to test the idea that enhancing or eliminating sexual selection would lead to variation in sex comb tooth number. However, the results showed no effect of either enforced monogamy or elevated promiscuity on this trait. We discuss several hypotheses to explain the lack of divergence, focussing on sexually antagonistic coevolution, stabilizing selection via species recognition and nonlinear selection. We discuss how these are important, but relatively ignored, alternatives in understanding the evolution of rapidly evolving sexually dimorphic traits. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Natural Selection as Coarsening

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2017-11-01

Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

Natural Selection as Coarsening

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2018-07-01

Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

How can we estimate natural selection on endocrine traits? Lessons from evolutionary biology

PubMed Central

2016-01-01

An evolutionary perspective can enrich almost any endeavour in biology, providing a deeper understanding of the variation we see in nature. To this end, evolutionary endocrinologists seek to describe the fitness consequences of variation in endocrine traits. Much of the recent work in our field, however, follows a flawed approach to the study of how selection shapes endocrine traits. Briefly, this approach relies on among-individual correlations between endocrine phenotypes (often circulating hormone levels) and fitness metrics to estimate selection on those endocrine traits. Adaptive plasticity in both endocrine and fitness-related traits can drive these correlations, generating patterns that do not accurately reflect natural selection. We illustrate why this approach to studying selection on endocrine traits is problematic, referring to work from evolutionary biologists who, decades ago, described this problem as it relates to a variety of other plastic traits. We extend these arguments to evolutionary endocrinology, where the likelihood that this flaw generates bias in estimates of selection is unusually high due to the exceptional responsiveness of hormones to environmental conditions, and their function to induce adaptive life-history responses to environmental variation. We end with a review of productive approaches for investigating the fitness consequences of variation in endocrine traits that we expect will generate exciting advances in our understanding of endocrine system evolution. PMID:27881753

Combining environment-driven adaptation and task-driven optimisation in evolutionary robotics.

PubMed

Haasdijk, Evert; Bredeche, Nicolas; Eiben, A E

2014-01-01

Embodied evolutionary robotics is a sub-field of evolutionary robotics that employs evolutionary algorithms on the robotic hardware itself, during the operational period, i.e., in an on-line fashion. This enables robotic systems that continuously adapt, and are therefore capable of (re-)adjusting themselves to previously unknown or dynamically changing conditions autonomously, without human oversight. This paper addresses one of the major challenges that such systems face, viz. that the robots must satisfy two sets of requirements. Firstly, they must continue to operate reliably in their environment (viability), and secondly they must competently perform user-specified tasks (usefulness). The solution we propose exploits the fact that evolutionary methods have two basic selection mechanisms-survivor selection and parent selection. This allows evolution to tackle the two sets of requirements separately: survivor selection is driven by the environment and parent selection is based on task-performance. This idea is elaborated in the Multi-Objective aNd open-Ended Evolution (monee) framework, which we experimentally validate. Experiments with robotic swarms of 100 simulated e-pucks show that monee does indeed promote task-driven behaviour without compromising environmental adaptation. We also investigate an extension of the parent selection process with a 'market mechanism' that can ensure equitable distribution of effort over multiple tasks, a particularly pressing issue if the environment promotes specialisation in single tasks.

Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians.

PubMed

Chamala, Srikar; Beckstead, Wesley A; Rowe, Mark J; McClellan, David A

2007-01-01

We investigated whether the effect of evolutionary selection on three recent Single Nucleotide Polymorphisms (SNPs) in the mitochondrial sub-haplogroups of Pima Indians is consistent with their effects on metabolic efficiency. The mitochondrial SNPs impact metabolic rate and respiratory quotient, and may be adaptations to caloric restriction in a desert habitat. Using TreeSAAP software, we examined evolutionary selection in 107 mammalian species at these SNPs, characterising the biochemical shifts produced by the amino acid substitutions. Our results suggest that two SNPs were affected by selection during mammalian evolution in a manner consistent with their effects on metabolic efficiency in Pima Indians.

Self-extinction through optimizing selection.

PubMed

Parvinen, Kalle; Dieckmann, Ulf

2013-09-21

Evolutionary suicide is a process in which selection drives a viable population to extinction. So far, such selection-driven self-extinction has been demonstrated in models with frequency-dependent selection. This is not surprising, since frequency-dependent selection can disconnect individual-level and population-level interests through environmental feedback. Hence it can lead to situations akin to the tragedy of the commons, with adaptations that serve the selfish interests of individuals ultimately ruining a population. For frequency-dependent selection to play such a role, it must not be optimizing. Together, all published studies of evolutionary suicide have created the impression that evolutionary suicide is not possible with optimizing selection. Here we disprove this misconception by presenting and analyzing an example in which optimizing selection causes self-extinction. We then take this line of argument one step further by showing, in a further example, that selection-driven self-extinction can occur even under frequency-independent selection. Copyright © 2013 Elsevier Ltd. All rights reserved.

The scope and strength of sex-specific selection in genome evolution

PubMed Central

Wright, A E; Mank, J E

2013-01-01

Males and females share the vast majority of their genomes and yet are often subject to different, even conflicting, selection. Genomic and transcriptomic developments have made it possible to assess sex-specific selection at the molecular level, and it is clear that sex-specific selection shapes the evolutionary properties of several genomic characteristics, including transcription, post-transcriptional regulation, imprinting, genome structure and gene sequence. Sex-specific selection is strongly influenced by mating system, which also causes neutral evolutionary changes that affect different regions of the genome in different ways. Here, we synthesize theoretical and molecular work in order to provide a cohesive view of the role of sex-specific selection and mating system in genome evolution. We also highlight the need for a combined approach, incorporating both genomic data and experimental phenotypic studies, in order to understand precisely how sex-specific selection drives evolutionary change across the genome. PMID:23848139

Divergent Evolutionary Pattern of Sugar Transporter Genes is Associated with the Difference in Sugar Accumulation between Grasses and Eudicots.

PubMed

Wang, Wei; Zhou, Hui; Ma, Baiquan; Owiti, Albert; Korban, Schuyler S; Han, Yuepeng

2016-06-30

Sugars play a variety of roles in plants, and their accumulation in seeds and/or surrounding pericarp tissues is distinctly different between grasses and eudicots. However, little is known about the evolutionary pattern of genes involved in sugar accumulation in these two major groups of flowering plants. Here, we compared evolutionary rates, gene duplication, and selective patterns of genes involved in sugar metabolism and transport between grasses and eudicots using six grass species and seven eudicot species as materials. Overall, sugar transporter genes exhibit divergent evolutionary patterns, whereas, sugar metabolism genes showing similar evolutionary pattern between monocots and eudicots. Sugar transporter genes have higher frequencies of recent duplication in eudicots than in grasses and their patterns of evolutionary rate are different. Evidence for divergent selection of these two groups of flowering plants is also observed in sugar transporter genes, wherein, these genes have undergone positive selection in eudicots, but not in grasses. Taken together, these findings suggest that sugar transporter genes rather than sugar metabolism genes play important roles in sugar accumulation in plants, and that divergent evolutionary patterns of sugar transporter genes are associated with the difference of sugar accumulation in storage tissues of grasses and eudicots.

Divergent Evolutionary Pattern of Sugar Transporter Genes is Associated with the Difference in Sugar Accumulation between Grasses and Eudicots

PubMed Central

Wang, Wei; Zhou, Hui; Ma, Baiquan; Owiti, Albert; Korban, Schuyler S.; Han, Yuepeng

2016-01-01

Sugars play a variety of roles in plants, and their accumulation in seeds and/or surrounding pericarp tissues is distinctly different between grasses and eudicots. However, little is known about the evolutionary pattern of genes involved in sugar accumulation in these two major groups of flowering plants. Here, we compared evolutionary rates, gene duplication, and selective patterns of genes involved in sugar metabolism and transport between grasses and eudicots using six grass species and seven eudicot species as materials. Overall, sugar transporter genes exhibit divergent evolutionary patterns, whereas, sugar metabolism genes showing similar evolutionary pattern between monocots and eudicots. Sugar transporter genes have higher frequencies of recent duplication in eudicots than in grasses and their patterns of evolutionary rate are different. Evidence for divergent selection of these two groups of flowering plants is also observed in sugar transporter genes, wherein, these genes have undergone positive selection in eudicots, but not in grasses. Taken together, these findings suggest that sugar transporter genes rather than sugar metabolism genes play important roles in sugar accumulation in plants, and that divergent evolutionary patterns of sugar transporter genes are associated with the difference of sugar accumulation in storage tissues of grasses and eudicots. PMID:27356489

Transmissible cancers in an evolutionary context.

PubMed

Ujvari, Beata; Papenfuss, Anthony T; Belov, Katherine

2016-07-01

Cancer is an evolutionary and ecological process in which complex interactions between tumour cells and their environment share many similarities with organismal evolution. Tumour cells with highest adaptive potential have a selective advantage over less fit cells. Naturally occurring transmissible cancers provide an ideal model system for investigating the evolutionary arms race between cancer cells and their surrounding micro-environment and macro-environment. However, the evolutionary landscapes in which contagious cancers reside have not been subjected to comprehensive investigation. Here, we provide a multifocal analysis of transmissible tumour progression and discuss the selection forces that shape it. We demonstrate that transmissible cancers adapt to both their micro-environment and macro-environment, and evolutionary theories applied to organisms are also relevant to these unique diseases. The three naturally occurring transmissible cancers, canine transmissible venereal tumour (CTVT) and Tasmanian devil facial tumour disease (DFTD) and the recently discovered clam leukaemia, exhibit different evolutionary phases: (i) CTVT, the oldest naturally occurring cell line is remarkably stable; (ii) DFTD exhibits the signs of stepwise cancer evolution; and (iii) clam leukaemia shows genetic instability. While all three contagious cancers carry the signature of ongoing and fairly recent adaptations to selective forces, CTVT appears to have reached an evolutionary stalemate with its host, while DFTD and the clam leukaemia appear to be still at a more dynamic phase of their evolution. Parallel investigation of contagious cancer genomes and transcriptomes and of their micro-environment and macro-environment could shed light on the selective forces shaping tumour development at different time points: during the progressive phase and at the endpoint. A greater understanding of transmissible cancers from an evolutionary ecology perspective will provide novel avenues for the prevention and treatment of both contagious and non-communicable cancers. © 2016 The Authors. BioEssays published by WILEY Periodicals, Inc.

Extrapolating Weak Selection in Evolutionary Games

PubMed Central

Wu, Bin; García, Julián; Hauert, Christoph; Traulsen, Arne

2013-01-01

In evolutionary games, reproductive success is determined by payoffs. Weak selection means that even large differences in game outcomes translate into small fitness differences. Many results have been derived using weak selection approximations, in which perturbation analysis facilitates the derivation of analytical results. Here, we ask whether results derived under weak selection are also qualitatively valid for intermediate and strong selection. By “qualitatively valid” we mean that the ranking of strategies induced by an evolutionary process does not change when the intensity of selection increases. For two-strategy games, we show that the ranking obtained under weak selection cannot be carried over to higher selection intensity if the number of players exceeds two. For games with three (or more) strategies, previous examples for multiplayer games have shown that the ranking of strategies can change with the intensity of selection. In particular, rank changes imply that the most abundant strategy at one intensity of selection can become the least abundant for another. We show that this applies already to pairwise interactions for a broad class of evolutionary processes. Even when both weak and strong selection limits lead to consistent predictions, rank changes can occur for intermediate intensities of selection. To analyze how common such games are, we show numerically that for randomly drawn two-player games with three or more strategies, rank changes frequently occur and their likelihood increases rapidly with the number of strategies . In particular, rank changes are almost certain for , which jeopardizes the predictive power of results derived for weak selection. PMID:24339769

Climbing Mount Probable

ERIC Educational Resources Information Center

Harper, Marc Allen

2009-01-01

This work attempts to explain the relationships between natural selection, information theory, and statistical inference. In particular, a geometric formulation of information theory known as information geometry and its deep connections to evolutionary game theory inform the role of natural selection in evolutionary processes. The goals of this…

Multigenerational response to artificial selection for biased clutch sex ratios in Tigriopus californicus populations.

PubMed

Alexander, H J; Richardson, J M L; Anholt, B R

2014-09-01

Polygenic sex determination (PSD) is relatively rare and theoretically evolutionary unstable, yet has been reported across a range of taxa. Evidence for multilocus PSD is provided by (i) large between-family variance in sex ratio, (ii) paternal and maternal effects on family sex ratio and (iii) response to selection for family sex ratio. This study tests the polygenic hypothesis of sex determination in the harpacticoid copepod Tigriopus californicus using the criterion of response to selection. We report the first multigenerational quantitative evidence that clutch sex ratio responds to artificial selection in both directions (selection for male- and female-biased families) and in multiple populations of T. californicus. In the five of six lines that showed a response to selection, realized heritability estimated by multigenerational analysis ranged from 0.24 to 0.58. Divergence of clutch sex ratio between selection lines is rapid, with response to selection detectable within the first four generations of selection. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Animal behaviour and algal camouflage jointly structure predation and selection.

PubMed

Start, Denon

2018-05-01

Trait variation can structure interactions between individuals, thus shaping selection. Although antipredator strategies are an important component of many aquatic systems, how multiple antipredator traits interact to influence consumption and selection remains contentious. Here, I use a common larval dragonfly (Epitheca canis) and its predator (Anax junius) to test for the joint effects of activity rate and algal camouflage on predation and survival selection. I found that active and poorly camouflaged Epitheca were more likely to be consumed, and thus, survival selection favoured inactive and well-camouflaged individuals. Notably, camouflage dampened selection on activity rate, likely by reducing attack rates when Epitheca encountered a predator. Correlational selection is therefore conferred by the ecological interaction of traits, rather than by opposing selection acting on linked traits. I suggest that antipredator traits with different adaptive functions can jointly structure patterns of consumption and selection. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

The long-term evolution of multilocus traits under frequency-dependent disruptive selection.

PubMed

van Doorn, G Sander; Dieckmann, Ulf

2006-11-01

Frequency-dependent disruptive selection is widely recognized as an important source of genetic variation. Its evolutionary consequences have been extensively studied using phenotypic evolutionary models, based on quantitative genetics, game theory, or adaptive dynamics. However, the genetic assumptions underlying these approaches are highly idealized and, even worse, predict different consequences of frequency-dependent disruptive selection. Population genetic models, by contrast, enable genotypic evolutionary models, but traditionally assume constant fitness values. Only a minority of these models thus addresses frequency-dependent selection, and only a few of these do so in a multilocus context. An inherent limitation of these remaining studies is that they only investigate the short-term maintenance of genetic variation. Consequently, the long-term evolution of multilocus characters under frequency-dependent disruptive selection remains poorly understood. We aim to bridge this gap between phenotypic and genotypic models by studying a multilocus version of Levene's soft-selection model. Individual-based simulations and deterministic approximations based on adaptive dynamics theory provide insights into the underlying evolutionary dynamics. Our analysis uncovers a general pattern of polymorphism formation and collapse, likely to apply to a wide variety of genetic systems: after convergence to a fitness minimum and the subsequent establishment of genetic polymorphism at multiple loci, genetic variation becomes increasingly concentrated on a few loci, until eventually only a single polymorphic locus remains. This evolutionary process combines features observed in quantitative genetics and adaptive dynamics models, and it can be explained as a consequence of changes in the selection regime that are inherent to frequency-dependent disruptive selection. Our findings demonstrate that the potential of frequency-dependent disruptive selection to maintain polygenic variation is considerably smaller than previously expected.

Induced defences alter the strength and direction of natural selection on reproductive traits in common milkweed.

PubMed

Thompson, K A; Cory, K A; Johnson, M T J

2017-06-01

Evolutionary biologists have long sought to understand the ecological processes that generate plant reproductive diversity. Recent evidence indicates that constitutive antiherbivore defences can alter natural selection on reproductive traits, but it is unclear whether induced defences will have the same effect and whether reduced foliar damage in defended plants is the cause of this pattern. In a factorial field experiment using common milkweed, Asclepias syriaca L., we induced plant defences using jasmonic acid (JA) and imposed foliar damage using scissors. We found that JA-induced plants experienced selection for more inflorescences that were smaller in size (fewer flowers), whereas control plants only experienced a trend towards selection for larger inflorescences (more flowers); all effects were independent of foliar damage. Our results demonstrate that induced defences can alter both the strength and direction of selection on reproductive traits, and suggest that antiherbivore defences may promote the evolution of plant reproductive diversity. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

The great struggles of life: Darwin and the emergence of evolutionary psychology.

PubMed

Buss, David M

2009-01-01

Darwin envisioned a scientific revolution for psychology. His theories of natural and sexual selection identified two classes of struggles--the struggle for existence and the struggle for mates. The emergence of evolutionary psychology and related disciplines signals the fulfillment of Darwin's vision. Natural selection theory guides scientists to discover adaptations for survival. Sexual selection theory illuminates the sexual struggle, highlighting mate choice and same-sex competition adaptations. Theoretical developments since publication of On the Origin of Species identify important struggles unknown to Darwin, notably, within-families conflicts and conflict between the sexes. Evolutionary psychology synthesizes modern evolutionary biology and psychology to penetrate some of life's deep mysteries: Why do many struggles center around sex? Why is social conflict pervasive? And what are the mechanisms of mind that define human nature? 2009 APA, all rights reserved

THE NICHE CONSTRUCTION PERSPECTIVE: A CRITICAL APPRAISAL*

PubMed Central

Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

2014-01-01

Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). PMID:24325256

The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

PubMed Central

Chen, Bor-Sen; Ho, Shih-Ju

2014-01-01

In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to an n-tuple evolutionary game of stochastic biological networks with m players (competitive populations) and k environmental dynamics. PMID:24558296

Natural selection. IV. The Price equation*

PubMed Central

Frank, Steven A.

2012-01-01

The Price equation partitions total evolutionary change into two components. The first component provides an abstract expression of natural selection. The second component subsumes all other evolutionary processes, including changes during transmission. The natural selection component is often used in applications. Those applications attract widespread interest for their simplicity of expression and ease of interpretation. Those same applications attract widespread criticism by dropping the second component of evolutionary change and by leaving unspecified the detailed assumptions needed for a complete study of dynamics. Controversies over approximation and dynamics have nothing to do with the Price equation itself, which is simply a mathematical equivalence relation for total evolutionary change expressed in an alternative form. Disagreements about approach have to do with the tension between the relative valuation of abstract versus concrete analyses. The Price equation’s greatest value has been on the abstract side, particularly the invariance relations that illuminate the understanding of natural selection. Those abstract insights lay the foundation for applications in terms of kin selection, information theory interpretations of natural selection, and partitions of causes by path analysis. I discuss recent critiques of the Price equation by Nowak and van Veelen. PMID:22487312

Classification of Medical Datasets Using SVMs with Hybrid Evolutionary Algorithms Based on Endocrine-Based Particle Swarm Optimization and Artificial Bee Colony Algorithms.

PubMed

Lin, Kuan-Cheng; Hsieh, Yi-Hsiu

2015-10-01

The classification and analysis of data is an important issue in today's research. Selecting a suitable set of features makes it possible to classify an enormous quantity of data quickly and efficiently. Feature selection is generally viewed as a problem of feature subset selection, such as combination optimization problems. Evolutionary algorithms using random search methods have proven highly effective in obtaining solutions to problems of optimization in a diversity of applications. In this study, we developed a hybrid evolutionary algorithm based on endocrine-based particle swarm optimization (EPSO) and artificial bee colony (ABC) algorithms in conjunction with a support vector machine (SVM) for the selection of optimal feature subsets for the classification of datasets. The results of experiments using specific UCI medical datasets demonstrate that the accuracy of the proposed hybrid evolutionary algorithm is superior to that of basic PSO, EPSO and ABC algorithms, with regard to classification accuracy using subsets with a reduced number of features.

Older partner selection promotes the prevalence of cooperation in evolutionary games.

PubMed

Yang, Guoli; Huang, Jincai; Zhang, Weiming

2014-10-21

Evolutionary games typically come with the interplays between evolution of individual strategy and adaptation to network structure. How these dynamics in the co-evolution promote (or obstruct) the cooperation is regarded as an important topic in social, economic, and biological fields. Combining spatial selection with partner choice, the focus of this paper is to identify which neighbour should be selected as a role to imitate during the process of co-evolution. Age, an internal attribute and kind of local piece of information regarding the survivability of the agent, is a significant consideration for the selection strategy. The analysis and simulations presented, demonstrate that older partner selection for strategy imitation could foster the evolution of cooperation. The younger partner selection, however, may decrease the level of cooperation. Our model highlights the importance of agent׳s age on the promotion of cooperation in evolutionary games, both efficiently and effectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evolutionary Perspectives on Genetic and Environmental Risk Factors for Psychiatric Disorders.

PubMed

Keller, Matthew C

2018-05-07

Evolutionary medicine uses evolutionary theory to help elucidate why humans are vulnerable to disease and disorders. I discuss two different types of evolutionary explanations that have been used to help understand human psychiatric disorders. First, a consistent finding is that psychiatric disorders are moderately to highly heritable, and many, such as schizophrenia, are also highly disabling and appear to decrease Darwinian fitness. Models used in evolutionary genetics to understand why genetic variation exists in fitness-related traits can be used to understand why risk alleles for psychiatric disorders persist in the population. The usual explanation for species-typical adaptations-natural selection-is less useful for understanding individual differences in genetic risk to disorders. Rather, two other types of models, mutation-selection-drift and balancing selection, offer frameworks for understanding why genetic variation in risk to psychiatric (and other) disorders exists, and each makes predictions that are now testable using whole-genome data. Second, species-typical capacities to mount reactions to negative events are likely to have been crafted by natural selection to minimize fitness loss. The pain reaction to tissue damage is almost certainly such an example, but it has been argued that the capacity to experience depressive symptoms such as sadness, anhedonia, crying, and fatigue in the face of adverse life situations may have been crafted by natural selection as well. I review the rationale and strength of evidence for this hypothesis. Evolutionary hypotheses of psychiatric disorders are important not only for offering explanations for why psychiatric disorders exist, but also for generating new, testable hypotheses and understanding how best to design studies and analyze data.

Social Media: Menagerie of Metrics

DTIC Science & Technology

2010-01-27

intelligence, an evolutionary algorithm (EA) is a subset of evolutionary computation, a generic population-based metaheuristic optimization algorithm . An EA...Cloning - 22 Animals were cloned to date; genetic algorithms can help prediction (e.g. “elitism” - attempts to ensure selection by including performers...28, 2010 Evolutionary Algorithm • Evolutionary algorithm From Wikipedia, the free encyclopedia Artificial intelligence portal In artificial

Selection on bristle length has the ability to drive the evolution of male abdominal appendages in the sepsid fly Themira biloba.

PubMed

Herath, B; Dochtermann, N A; Johnson, J I; Leonard, Z; Bowsher, J H

2015-12-01

Many exaggerated and novel traits are strongly influenced by sexual selection. Although sexual selection is a powerful evolutionary force, underlying genetic interactions can constrain evolutionary outcomes. The relative strength of selection vs. constraint has been a matter of debate for the evolution of male abdominal appendages in sepsid flies. These abdominal appendages are involved in courtship and mating, but their function has not been directly tested. We performed mate choice experiments to determine whether sexual selection acts on abdominal appendages in the sepsid Themira biloba. We tested whether appendage bristle length influenced successful insemination by surgically trimming the bristles. Females paired with males that had shortened bristles laid only unfertilized eggs, indicating that long bristles are necessary for successful insemination. We also tested whether the evolution of bristle length was constrained by phenotypic correlations with other traits. Analyses of phenotypic covariation indicated that bristle length was highly correlated with other abdominal appendage traits, but was not correlated with abdominal sternite size. Thus, abdominal appendages are not exaggerated traits like many sexual ornaments, but vary independently from body size. At the same time, strong correlations between bristle length and appendage length suggest that selection on bristle length is likely to result in a correlated increase in appendage length. Bristle length is under sexual selection in T. biloba and has the potential to evolve independently from abdomen size. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

PubMed Central

Sheng, Zizhang; Schramm, Chaim A.; Connors, Mark; Morris, Lynn; Mascola, John R.; Kwong, Peter D.; Shapiro, Lawrence

2016-01-01

Accumulation of somatic mutations in antibody variable regions is critical for antibody affinity maturation, with HIV-1 broadly neutralizing antibodies (bnAbs) generally requiring years to develop. We recently found that the rate at which mutations accumulate decreases over time, but the mechanism governing this slowing is unclear. In this study, we investigated whether natural selection and/or mutability of the antibody variable region contributed significantly to observed decrease in rate. We used longitudinally sampled sequences of immunoglobulin transcripts of single lineages from each of 3 donors, as determined by next generation sequencing. We estimated the evolutionary rates of the complementarity determining regions (CDRs), which are most significant for functional selection, and found they evolved about 1.5- to 2- fold faster than the framework regions. We also analyzed the presence of AID hotspots and coldspots at different points in lineage development and observed an average decrease in mutability of less than 10 percent over time. Altogether, the correlation between Darwinian selection strength and evolutionary rate trended toward significance, especially for CDRs, but cannot fully explain the observed changes in evolutionary rate. The mutability modulated by AID hotspots and coldspots changes correlated only weakly with evolutionary rates. The combined effects of Darwinian selection and mutability contribute substantially to, but do not fully explain, evolutionary rate change for HIV-1-targeting bnAb lineages. PMID:27191167

Artificial selection on ant female caste ratio uncovers a link between female-biased sex ratios and infection by Wolbachia endosymbionts.

PubMed

Pontieri, L; Schmidt, A M; Singh, R; Pedersen, J S; Linksvayer, T A

2017-02-01

Social insect sex and caste ratios are well-studied targets of evolutionary conflicts, but the heritable factors affecting these traits remain unknown. To elucidate these factors, we carried out a short-term artificial selection study on female caste ratio in the ant Monomorium pharaonis. Across three generations of bidirectional selection, we observed no response for caste ratio, but sex ratios rapidly became more female-biased in the two replicate high selection lines and less female-biased in the two replicate low selection lines. We hypothesized that this rapid divergence for sex ratio was caused by changes in the frequency of infection by the heritable bacterial endosymbiont Wolbachia, because the initial breeding stock varied for Wolbachia infection, and Wolbachia is known to cause female-biased sex ratios in other insects. Consistent with this hypothesis, the proportions of Wolbachia-infected colonies in the selection lines changed rapidly, mirroring the sex ratio changes. Moreover, the estimated effect of Wolbachia on sex ratio (~13% female bias) was similar in colonies before and during artificial selection, indicating that this Wolbachia effect is likely independent of the effects of artificial selection on other heritable factors. Our study provides evidence for the first case of endosymbiont sex ratio manipulation in a social insect. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Darwin's "Imaginary Illustrations": Creatively Teaching Evolutionary Concepts & the Nature of Science

ERIC Educational Resources Information Center

Love, Alan C.

2010-01-01

An overlooked feature of Darwin's work is his use of "imaginary illustrations" to show that natural selection is competent to produce adaptive, evolutionary change. When set in the context of Darwin's methodology, these thought experiments provide a novel way to teach natural selection and the nature of science.

Telling Tales at Work: An Evolutionary Explanation

ERIC Educational Resources Information Center

Yang, Chulguen

2013-01-01

This article explores the adaptive functions of storytelling in the workplace from an evolutionary perspective. Based on the analysis of ethnographic studies on hunter-gatherer and modern work organizations, this article claims that storytelling, as an adapted cognitive device, was selectively retained by natural and sexual selection, because of…

Optimal Wavelengths Selection Using Hierarchical Evolutionary Algorithm for Prediction of Firmness and Soluble Solids Content in Apples

USDA-ARS?s Scientific Manuscript database

Hyperspectral scattering is a promising technique for rapid and noninvasive measurement of multiple quality attributes of apple fruit. A hierarchical evolutionary algorithm (HEA) approach, in combination with subspace decomposition and partial least squares (PLS) regression, was proposed to select o...

Adaptive Memory: Young Children Show Enhanced Retention of Fitness-Related Information

ERIC Educational Resources Information Center

Aslan, Alp; Bauml, Karl-Heinz T.

2012-01-01

Evolutionary psychologists propose that human cognition evolved through natural selection to solve adaptive problems related to survival and reproduction, with its ultimate function being the enhancement of reproductive fitness. Following this proposal and the evolutionary-developmental view that ancestral selection pressures operated not only on…

Optimality and stability of symmetric evolutionary games with applications in genetic selection.

PubMed

Huang, Yuanyuan; Hao, Yiping; Wang, Min; Zhou, Wen; Wu, Zhijun

2015-06-01

Symmetric evolutionary games, i.e., evolutionary games with symmetric fitness matrices, have important applications in population genetics, where they can be used to model for example the selection and evolution of the genotypes of a given population. In this paper, we review the theory for obtaining optimal and stable strategies for symmetric evolutionary games, and provide some new proofs and computational methods. In particular, we review the relationship between the symmetric evolutionary game and the generalized knapsack problem, and discuss the first and second order necessary and sufficient conditions that can be derived from this relationship for testing the optimality and stability of the strategies. Some of the conditions are given in different forms from those in previous work and can be verified more efficiently. We also derive more efficient computational methods for the evaluation of the conditions than conventional approaches. We demonstrate how these conditions can be applied to justifying the strategies and their stabilities for a special class of genetic selection games including some in the study of genetic disorders.

Algorithmic Mechanism Design of Evolutionary Computation.

PubMed

Pei, Yan

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm.

Algorithmic Mechanism Design of Evolutionary Computation

PubMed Central

2015-01-01

We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777

Selection on female behaviour fluctuates with offspring environment.

PubMed

Taylor, R W; Boutin, S; Humphries, M M; McAdam, A G

2014-11-01

Temporal variation in selection has long been proposed as a mechanism by which genetic variation could be maintained despite short-term strong directional selection and has been invoked to explain the maintenance of consistent individual differences in behaviour. We tested the hypothesis that ecological changes through time lead to fluctuating selection, which could promote the maintenance of variation in female behavioural traits in a wild population of North American red squirrels. As predicted, linear selection gradients on female aggression and activity significantly fluctuated across years depending on the level of competition among juveniles for vacant territories. This selection acted primarily through juvenile overwinter survival rather than maternal fecundity. Incorporating uncertainty in individual measures of behaviour reduced the magnitude of annual selection gradients and increased uncertainty in these estimates, but did not affect the overall pattern of temporal fluctuations in natural selection that coincided with the intensity of competition for vacant territories. These temporal fluctuations in selection might, therefore, promote the maintenance of heritable individual differences in behaviour in this wild red squirrel population. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

The consequences of lifetime and evolutionary exposure to toxic prey: changes in avoidance behaviour through ontogeny.

PubMed

Robbins, T R; Langkilde, T

2012-10-01

Responses to novel threats (e.g. invasive species) can involve genetic changes or plastic shifts in phenotype. There is controversy over the relative importance of these processes for species survival of such perturbations, but we are realizing they are not mutually exclusive. Native eastern fence lizards (Sceloporus undulatus) have adapted to top-down predation pressure imposed by the invasive red imported fire ant (Solenopsis invicta) via changes in adult (but not juvenile) lizard antipredator behaviour. Here, we examine the largely ignored, but potentially equally important, bottom-up effect of fire ants as toxic prey for lizards. We test how fire ant consumption (or avoidance) is affected by lifetime (via plasticity) and evolutionary (via natural selection) exposure to fire ants by comparing field-caught and laboratory-reared lizards, respectively, from fire ant-invaded and uninvaded populations. More naive juveniles from invaded populations ate fire ants than did adults, reflecting a natural ontogenetic dietary shift away from ants. Laboratory-reared lizards from the invaded site were less likely to eat fire ants than were those from the uninvaded site, suggesting a potential evolutionary shift in feeding behaviour. Lifetime and evolutionary exposure interacted across ontogeny, however, and field-caught lizards from the invaded site exhibited opposite ontogenetic trends; adults were more likely to eat fire ants than were juveniles. Our results suggest that plastic and evolutionary processes may both play important roles in permitting species survival of novel threats. We further reveal how complex interactions can shape adaptive responses to multimodal impacts imposed by invaders: in our system, fire ants impose stronger bottom-up selection than top-down selection, with each selection regime changing differently across lizard ontogeny. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Strategic Reality and Tactical Mirages: Special Operations and the Iranian Hostage Rescue, 1979-1980

DTIC Science & Technology

2017-06-01

additional error. The noise of C -130 engines and whirling helicopter blades made communication nearly impossible at the loading site and added...first chapter will provide an historical overview of Operation Eagle Claw. The narrative conveys what shaped the military and geopolitical environment...of RH-53D helicopters and C -130 aircraft as the best and only mix of assets to overcome the tyranny of distance—the 865 nautical mile flight is the

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses.

PubMed

Furuse, Yuki; Matsuzaki, Yoko; Nishimura, Hidekazu; Oshitani, Hitoshi

2016-11-26

Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses

PubMed Central

Furuse, Yuki; Matsuzaki, Yoko; Nishimura, Hidekazu; Oshitani, Hitoshi

2016-01-01

Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics. PMID:27898037

The niche construction perspective: a critical appraisal.

PubMed

Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

2014-05-01

Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). © 2013 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Experimentally evolved and phenotypically plastic responses to enforced monogamy in a hermaphroditic flatworm.

PubMed

Janicke, T; Sandner, P; Ramm, S A; Vizoso, D B; Schärer, L

2016-09-01

Sexual selection is considered a potent evolutionary force in all sexually reproducing organisms, but direct tests in terms of experimental evolution of sexual traits are still lacking for simultaneously hermaphroditic animals. Here, we tested how evolution under enforced monogamy affected a suite of reproductive traits (including testis area, sex allocation, genital morphology, sperm morphology and mating behaviour) in the outcrossing hermaphroditic flatworm Macrostomum lignano, using an assay that also allowed the assessment of phenotypically plastic responses to group size. The experiment comprised 32 independent selection lines that evolved under either monogamy or polygamy for 20 generations. While we did not observe an evolutionary shift in sex allocation, we detected effects of the selection regime for two male morphological traits. Specifically, worms evolving under enforced monogamy had a distinct shape of the male copulatory organ and produced sperm with shorter appendages. Many traits that did not evolve under enforced monogamy showed phenotypic plasticity in response to group size. Notably, individuals that grew up in larger groups had a more male-biased sex allocation and produced slightly longer sperm than individuals raised in pairs. We conclude that, in this flatworm, enforced monogamy induced moderate evolutionary but substantial phenotypically plastic responses. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Integrating Evolutionary and Molecular Genetics of Aging

PubMed Central

Flatt, Thomas; Schmidt, Paul S.

2010-01-01

Aging or senescence is an age-dependent decline in physiological function, demographically manifest as decreased survival and fecundity with increasing age. Since aging is disadvantageous it should not evolve by natural selection. So why do organisms age and die? In the 1940’s and 1950’s evolutionary geneticists resolved this paradox by positing that aging evolves because selection is inefficient at maintaining function late in life. By the 1980’s and 1990’s this evolutionary theory of aging had received firm empirical support, but little was known about the mechanisms of aging. Around the same time biologists began to apply the tools of molecular genetics to aging and successfully identified mutations that affect longevity. Today, the molecular genetics of aging is a burgeoning field, but progress in evolutionary genetics of aging has largely stalled. Here we argue that some of the most exciting and unresolved questions about aging require an integration of molecular and evolutionary approaches. Is aging a universal process? Why do species age at different rates? Are the mechanisms of aging conserved or lineage-specific? Are longevity genes identified in the laboratory under selection in natural populations? What is the genetic basis of plasticity in aging in response to environmental cues and is this plasticity adaptive? What are the mechanisms underlying trade-offs between early fitness traits and life span? To answer these questions evolutionary biologists must adopt the tools of molecular biology, while molecular biologists must put their experiments into an evolutionary framework. The time is ripe for a synthesis of molecular biogerontology and the evolutionary biology of aging. PMID:19619612

Integrating evolutionary and molecular genetics of aging.

PubMed

Flatt, Thomas; Schmidt, Paul S

2009-10-01

Aging or senescence is an age-dependent decline in physiological function, demographically manifest as decreased survival and fecundity with increasing age. Since aging is disadvantageous it should not evolve by natural selection. So why do organisms age and die? In the 1940s and 1950s evolutionary geneticists resolved this paradox by positing that aging evolves because selection is inefficient at maintaining function late in life. By the 1980s and 1990s this evolutionary theory of aging had received firm empirical support, but little was known about the mechanisms of aging. Around the same time biologists began to apply the tools of molecular genetics to aging and successfully identified mutations that affect longevity. Today, the molecular genetics of aging is a burgeoning field, but progress in evolutionary genetics of aging has largely stalled. Here we argue that some of the most exciting and unresolved questions about aging require an integration of molecular and evolutionary approaches. Is aging a universal process? Why do species age at different rates? Are the mechanisms of aging conserved or lineage-specific? Are longevity genes identified in the laboratory under selection in natural populations? What is the genetic basis of plasticity in aging in response to environmental cues and is this plasticity adaptive? What are the mechanisms underlying trade-offs between early fitness traits and life span? To answer these questions evolutionary biologists must adopt the tools of molecular biology, while molecular biologists must put their experiments into an evolutionary framework. The time is ripe for a synthesis of molecular biogerontology and the evolutionary biology of aging.

Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords.

PubMed

Bentley, R Alexander

2008-08-27

The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.

Random Drift versus Selection in Academic Vocabulary: An Evolutionary Analysis of Published Keywords

PubMed Central

Bentley, R. Alexander

2008-01-01

The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example. PMID:18728786

Spatial Selection and Local Adaptation Jointly Shape Life-History Evolution during Range Expansion.

PubMed

Van Petegem, Katrien H P; Boeye, Jeroen; Stoks, Robby; Bonte, Dries

2016-11-01

In the context of climate change and species invasions, range shifts increasingly gain attention because the rates at which they occur in the Anthropocene induce rapid changes in biological assemblages. During range shifts, species experience multiple selection pressures. For poleward expansions in particular, it is difficult to interpret observed evolutionary dynamics because of the joint action of evolutionary processes related to spatial selection and to adaptation toward local climatic conditions. To disentangle the effects of these two processes, we integrated stochastic modeling and data from a common garden experiment, using the spider mite Tetranychus urticae as a model species. By linking the empirical data with those derived form a highly parameterized individual-based model, we infer that both spatial selection and local adaptation contributed to the observed latitudinal life-history divergence. Spatial selection best described variation in dispersal behavior, while variation in development was best explained by adaptation to the local climate. Divergence in life-history traits in species shifting poleward could consequently be jointly determined by contemporary evolutionary dynamics resulting from adaptation to the environmental gradient and from spatial selection. The integration of modeling with common garden experiments provides a powerful tool to study the contribution of these evolutionary processes on life-history evolution during range expansion.

Evolutionary stasis in Euphorbiaceae pollen: selection and constraints.

PubMed

Matamoro-Vidal, A; Furness, C A; Gouyon, P-H; Wurdack, K J; Albert, B

2012-06-01

Although much attention has been paid to the role of stabilizing selection, empirical analyses testing the role of developmental constraints in evolutionary stasis remain rare, particularly for plants. This topic is studied here with a focus on the evolution of a pollen ontogenetic feature, the last points of callose deposition (LPCD) pattern, involved in the determination of an adaptive morphological pollen character (aperture pattern). The LPCD pattern exhibits a low level of evolution in eudicots, as compared to the evolution observed in monocots. Stasis in this pattern might be explained by developmental constraints expressed during male meiosis (microsporogenesis) or by selective pressures expressed through the adaptive role of the aperture pattern. Here, we demonstrate that the LPCD pattern is conserved in Euphorbiaceae s.s. and that this conservatism is primarily due to selective pressures. A phylogenetic association was found between the putative removal of selective pressures on pollen morphology after the origin of inaperturate pollen, and the appearance of variation in microsporogenesis and in the resulting LPCD pattern, suggesting that stasis was due to these selective pressures. However, even in a neutral context, variation in microsporogenesis was biased. This should therefore favour the appearance of some developmental and morphological phenotypes rather than others. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Evolving Better Cars: Teaching Evolution by Natural Selection with a Digital Inquiry Activity

ERIC Educational Resources Information Center

Royer, Anne M.; Schultheis, Elizabeth H.

2014-01-01

Evolutionary experiments are usually difficult to perform in the classroom because of the large sizes and long timescales of experiments testing evolutionary hypotheses. Computer applications give students a window to observe evolution in action, allowing them to gain comfort with the process of natural selection and facilitating inquiry…

Investigating Undergraduate Students' Use of Intuitive Reasoning and Evolutionary Knowledge in Explanations of Antibiotic Resistance

ERIC Educational Resources Information Center

Richard, Melissa; Coley, John D.; Tanner, Kimberly D.

2017-01-01

Natural selection is a central concept throughout biology; however, it is a process frequently misunderstood. Bacterial resistance to antibiotic medications provides a contextual example of the relevance of evolutionary theory and is also commonly misunderstood. While research has shed light on student misconceptions of natural selection, minimal…

The Great Struggles of Life: Darwin and the Emergence of Evolutionary Psychology

ERIC Educational Resources Information Center

Buss, David M.

2009-01-01

Darwin envisioned a scientific revolution for psychology. His theories of natural and sexual selection identified two classes of struggles--the struggle for existence and the struggle for mates. The emergence of evolutionary psychology and related disciplines signals the fulfillment of Darwin's vision. Natural selection theory guides scientists to…

Subtle but ubiquitous selection on body size in a natural population of collared flycatchers over 33 years.

PubMed

Björklund, M; Gustafsson, L

2017-07-01

Understanding the magnitude and long-term patterns of selection in natural populations is of importance, for example, when analysing the evolutionary impact of climate change. We estimated univariate and multivariate directional, quadratic and correlational selection on four morphological traits (adult wing, tarsus and tail length, body mass) over a time period of 33 years (≈ 19 000 observations) in a nest-box breeding population of collared flycatchers (Ficedula albicollis). In general, selection was weak in both males and females over the years regardless of fitness measure (fledged young, recruits and survival) with only few cases with statistically significant selection. When data were analysed in a multivariate context and as time series, a number of patterns emerged; there was a consistent, but weak, selection for longer wings in both sexes, selection was stronger on females when the number of fledged young was used as a fitness measure, there were no indications of sexually antagonistic selection, and we found a negative correlation between selection on tarsus and wing length in both sexes but using different fitness measures. Uni- and multivariate selection gradients were correlated only for wing length and mass. Multivariate selection gradient vectors were longer than corresponding vector of univariate gradients and had more constrained direction. Correlational selection had little importance. Overall, the fitness surface was more or less flat with few cases of significant curvature, indicating that the adaptive peak with regard to body size in this species is broader than the phenotypic distribution, which has resulted in weak estimates of selection. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

The Creativity of Natural Selection? Part I: Darwin, Darwinism, and the Mutationists.

PubMed

Beatty, John

2016-12-01

This is the first of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. Here I focus on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled "mutationists." The second part focuses on the evolutionary synthesis and some of its critics, especially the "neutralists" and "neo-mutationists." Like Stephen Gould, I consider the creativity of natural selection to be a key component of what has traditionally counted as "Darwinism." I argue that the creativity of natural selection is best understood in terms of (1) selection initiating evolutionary change, and (2) selection being responsible for the presence of the variation it acts upon, for example by directing the course of variation. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism.

Evolutionary computation in zoology and ecology.

PubMed

Boone, Randall B

2017-12-01

Evolutionary computational methods have adopted attributes of natural selection and evolution to solve problems in computer science, engineering, and other fields. The method is growing in use in zoology and ecology. Evolutionary principles may be merged with an agent-based modeling perspective to have individual animals or other agents compete. Four main categories are discussed: genetic algorithms, evolutionary programming, genetic programming, and evolutionary strategies. In evolutionary computation, a population is represented in a way that allows for an objective function to be assessed that is relevant to the problem of interest. The poorest performing members are removed from the population, and remaining members reproduce and may be mutated. The fitness of the members is again assessed, and the cycle continues until a stopping condition is met. Case studies include optimizing: egg shape given different clutch sizes, mate selection, migration of wildebeest, birds, and elk, vulture foraging behavior, algal bloom prediction, and species richness given energy constraints. Other case studies simulate the evolution of species and a means to project shifts in species ranges in response to a changing climate that includes competition and phenotypic plasticity. This introduction concludes by citing other uses of evolutionary computation and a review of the flexibility of the methods. For example, representing species' niche spaces subject to selective pressure allows studies on cladistics, the taxon cycle, neutral versus niche paradigms, fundamental versus realized niches, community structure and order of colonization, invasiveness, and responses to a changing climate.

Evolutionary computation in zoology and ecology

PubMed Central

2017-01-01

Abstract Evolutionary computational methods have adopted attributes of natural selection and evolution to solve problems in computer science, engineering, and other fields. The method is growing in use in zoology and ecology. Evolutionary principles may be merged with an agent-based modeling perspective to have individual animals or other agents compete. Four main categories are discussed: genetic algorithms, evolutionary programming, genetic programming, and evolutionary strategies. In evolutionary computation, a population is represented in a way that allows for an objective function to be assessed that is relevant to the problem of interest. The poorest performing members are removed from the population, and remaining members reproduce and may be mutated. The fitness of the members is again assessed, and the cycle continues until a stopping condition is met. Case studies include optimizing: egg shape given different clutch sizes, mate selection, migration of wildebeest, birds, and elk, vulture foraging behavior, algal bloom prediction, and species richness given energy constraints. Other case studies simulate the evolution of species and a means to project shifts in species ranges in response to a changing climate that includes competition and phenotypic plasticity. This introduction concludes by citing other uses of evolutionary computation and a review of the flexibility of the methods. For example, representing species’ niche spaces subject to selective pressure allows studies on cladistics, the taxon cycle, neutral versus niche paradigms, fundamental versus realized niches, community structure and order of colonization, invasiveness, and responses to a changing climate. PMID:29492029

Universality and predictability in molecular quantitative genetics.

PubMed

Nourmohammad, Armita; Held, Torsten; Lässig, Michael

2013-12-01

Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. We review recent developments in evolutionary theory and experiments that are expected to become building blocks of a quantitative genetics of molecular traits. We focus on universal evolutionary characteristics: these are largely independent of a trait's genetic basis, which is often at least partially unknown. We show that universal measurements can be used to infer selection on a quantitative trait, which determines its evolutionary mode of conservation or adaptation. Furthermore, universality is closely linked to predictability of trait evolution across lineages. We argue that universal trait statistics extends over a range of cellular scales and opens new avenues of quantitative evolutionary systems biology. Copyright © 2013. Published by Elsevier Ltd.

Genes under weaker stabilizing selection increase network evolvability and rapid regulatory adaptation to an environmental shift.

PubMed

Laarits, T; Bordalo, P; Lemos, B

2016-08-01

Regulatory networks play a central role in the modulation of gene expression, the control of cellular differentiation, and the emergence of complex phenotypes. Regulatory networks could constrain or facilitate evolutionary adaptation in gene expression levels. Here, we model the adaptation of regulatory networks and gene expression levels to a shift in the environment that alters the optimal expression level of a single gene. Our analyses show signatures of natural selection on regulatory networks that both constrain and facilitate rapid evolution of gene expression level towards new optima. The analyses are interpreted from the standpoint of neutral expectations and illustrate the challenge to making inferences about network adaptation. Furthermore, we examine the consequence of variable stabilizing selection across genes on the strength and direction of interactions in regulatory networks and in their subsequent adaptation. We observe that directional selection on a highly constrained gene previously under strong stabilizing selection was more efficient when the gene was embedded within a network of partners under relaxed stabilizing selection pressure. The observation leads to the expectation that evolutionarily resilient regulatory networks will contain optimal ratios of genes whose expression is under weak and strong stabilizing selection. Altogether, our results suggest that the variable strengths of stabilizing selection across genes within regulatory networks might itself contribute to the long-term adaptation of complex phenotypes. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.

PubMed

Funk, W Chris; Murphy, Melanie A

2010-02-01

Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence (Garant et al. 2007) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation (Coyne & Orr 2004). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica (Fig. 1). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation-by-distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.

Modelling the influence of parental effects on gene-network evolution.

PubMed

Odorico, Andreas; Rünneburger, Estelle; Le Rouzic, Arnaud

2018-05-01

Understanding the importance of nongenetic heredity in the evolutionary process is a major topic in modern evolutionary biology. We modified a classical gene-network model by allowing parental transmission of gene expression and studied its evolutionary properties through individual-based simulations. We identified ontogenetic time (i.e. the time gene networks have to stabilize before being submitted to natural selection) as a crucial factor in determining the evolutionary impact of this phenotypic inheritance. Indeed, fast-developing organisms display enhanced adaptation and greater robustness to mutations when evolving in presence of nongenetic inheritance (NGI). In contrast, in our model, long development reduces the influence of the inherited state of the gene network. NGI thus had a negligible effect on the evolution of gene networks when the speed at which transcription levels reach equilibrium is not constrained. Nevertheless, simulations show that intergenerational transmission of the gene-network state negatively affects the evolution of robustness to environmental disturbances for either fast- or slow-developing organisms. Therefore, these results suggest that the evolutionary consequences of NGI might not be sought only in the way species respond to selection, but also on the evolution of emergent properties (such as environmental and genetic canalization) in complex genetic architectures. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

PubMed

Chen, Bor-Sen; Yeh, Chin-Hsun

2017-12-01

We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

Understanding the mind from an evolutionary perspective: an overview of evolutionary psychology.

PubMed

Shackelford, Todd K; Liddle, James R

2014-05-01

The theory of evolution by natural selection provides the only scientific explanation for the existence of complex adaptations. The design features of the brain, like any organ, are the result of selection pressures operating over deep time. Evolutionary psychology posits that the human brain comprises a multitude of evolved psychological mechanisms, adaptations to specific and recurrent problems of survival and reproduction faced over human evolutionary history. Although some mistakenly view evolutionary psychology as promoting genetic determinism, evolutionary psychologists appreciate and emphasize the interactions between genes and environments. This approach to psychology has led to a richer understanding of a variety of psychological phenomena, and has provided a powerful foundation for generating novel hypotheses. Critics argue that evolutionary psychologists resort to storytelling, but as with any branch of science, empirical testing is a vital component of the field, with hypotheses standing or falling with the weight of the evidence. Evolutionary psychology is uniquely suited to provide a unifying theoretical framework for the disparate subdisciplines of psychology. An evolutionary perspective has provided insights into several subdisciplines of psychology, while simultaneously demonstrating the arbitrary nature of dividing psychological science into such subdisciplines. Evolutionary psychologists have amassed a substantial empirical and theoretical literature, but as a relatively new approach to psychology, many questions remain, with several promising directions for future research. For further resources related to this article, please visit the WIREs website. The authors have declared no conflicts of interest for this article. © 2014 John Wiley & Sons, Ltd.

Molecular selection in a unified evolutionary sequence

NASA Technical Reports Server (NTRS)

Fox, S. W.

1986-01-01

With guidance from experiments and observations that indicate internally limited phenomena, an outline of unified evolutionary sequence is inferred. Such unification is not visible for a context of random matrix and random mutation. The sequence proceeds from Big Bang through prebiotic matter, protocells, through the evolving cell via molecular and natural selection, to mind, behavior, and society.

British and French Strategic Nuclear Force Modernization: Programs, Strategies, and Implications

DTIC Science & Technology

1989-12-01

Union . In addition 18 Mirage IVs will be fitted with ASMP (Air-Sol Moyenne Port’e) medium-range air to ground missiles with increased standoff capability...Chevaline upgrade to the Polaris A3 missiles in 1972 following the signing of the ABM Treaty between the United States and Soviet Union . This decision...Royal Navy Headquarters at Northwood to its Polaris submarines the U.K. relies upon three VLF (very low frequency) transmitters at 24 CrIgglon, Rugby

Nature's optics and our understanding of light

NASA Astrophysics Data System (ADS)

Berry, M. V.

2015-01-01

Optical phenomena visible to everyone have been central to the development of, and abundantly illustrate, important concepts in science and mathematics. The phenomena considered from this viewpoint are rainbows, sparkling reflections on water, mirages, green flashes, earthlight on the moon, glories, daylight, crystals and the squint moon. And the concepts involved include refraction, caustics (focal singularities of ray optics), wave interference, numerical experiments, mathematical asymptotics, dispersion, complex angular momentum (Regge poles), polarisation singularities, Hamilton's conical intersections of eigenvalues ('Dirac points'), geometric phases and visual illusions.

The diversification of Heliconius butterflies: what have we learned in 150 years?

PubMed

Merrill, R M; Dasmahapatra, K K; Davey, J W; Dell'Aglio, D D; Hanly, J J; Huber, B; Jiggins, C D; Joron, M; Kozak, K M; Llaurens, V; Martin, S H; Montgomery, S H; Morris, J; Nadeau, N J; Pinharanda, A L; Rosser, N; Thompson, M J; Vanjari, S; Wallbank, R W R; Yu, Q

2015-08-01

Research into Heliconius butterflies has made a significant contribution to evolutionary biology. Here, we review our understanding of the diversification of these butterflies, covering recent advances and a vast foundation of earlier work. Whereas no single group of organisms can be sufficient for understanding life's diversity, after years of intensive study, research into Heliconius has addressed a wide variety of evolutionary questions. We first discuss evidence for widespread gene flow between Heliconius species and what this reveals about the nature of species. We then address the evolution and diversity of warning patterns, both as the target of selection and with respect to their underlying genetic basis. The identification of major genes involved in mimetic shifts, and homology at these loci between distantly related taxa, has revealed a surprising predictability in the genetic basis of evolution. In the final sections, we consider the evolution of warning patterns, and Heliconius diversity more generally, within a broader context of ecological and sexual selection. We consider how different traits and modes of selection can interact and influence the evolution of reproductive isolation. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

An obligate brood parasite trapped in the intraspecific arms race of its hosts.

PubMed

Lyon, Bruce E; Eadie, John McA

2004-11-18

Reciprocal selection pressures often lead to close and adaptive matching of traits in coevolved species. A failure of one species to match the evolutionary trajectories of another is often attributed to evolutionary lags or to differing selection pressures across a geographic mosaic. Here we show that mismatches in adaptation of interacting species--an obligate brood parasitic duck and each of its two main hosts--are best explained by the evolutionary dynamics within the host species. Rejection of the brood parasite's eggs was common by both hosts, despite a lack of detectable cost of parasitism to the hosts. Egg rejection markedly reduced parasite fitness, but egg mimicry experiments revealed no phenotypic natural selection for more mimetic parasitic eggs. These paradoxical results were resolved by the discovery of intraspecific brood parasitism and conspecific egg rejection within the hosts themselves. The apparent arms race between species seems instead to be an incidental by-product of within-species conflict, with little recourse for evolutionary response by the parasite.

Antagonistic versus non-antagonistic models of balancing selection: Characterizing the relative timescales and hitchhiking effects of partial selective sweeps

PubMed Central

Connallon, Tim; Clark, Andrew G.

2012-01-01

Antagonistically selected alleles -- those with opposing fitness effects between sexes, environments, or fitness components -- represent an important component of additive genetic variance in fitness-related traits, with stably balanced polymorphisms often hypothesized to contribute to observed quantitative genetic variation. Balancing selection hypotheses imply that intermediate-frequency alleles disproportionately contribute to genetic variance of life history traits and fitness. Such alleles may also associate with population genetic footprints of recent selection, including reduced genetic diversity and inflated linkage disequilibrium at linked, neutral sites. Here, we compare the evolutionary dynamics of different balancing selection models, and characterize the evolutionary timescale and hitchhiking effects of partial selective sweeps generated under antagonistic versus non-antagonistic (e.g., overdominant and frequency-dependent selection) processes. We show that that the evolutionary timescales of partial sweeps tend to be much longer, and hitchhiking effects are drastically weaker, under scenarios of antagonistic selection. These results predict an interesting mismatch between molecular population genetic and quantitative genetic patterns of variation. Balanced, antagonistically selected alleles are expected to contribute more to additive genetic variance for fitness than alleles maintained by classic, non-antagonistic mechanisms. Nevertheless, classical mechanisms of balancing selection are much more likely to generate strong population genetic signatures of recent balancing selection. PMID:23461340

Breeding novel solutions in the brain: a model of Darwinian neurodynamics.

PubMed

Szilágyi, András; Zachar, István; Fedor, Anna; de Vladar, Harold P; Szathmáry, Eörs

2016-01-01

Background : The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the brain. Methods : We combine known components of the brain - recurrent neural networks (acting as attractors), the action selection loop and implicit working memory - to provide the appropriate Darwinian architecture. We employ a population of attractor networks with palimpsest memory. The action selection loop is employed with winners-share-all dynamics to select for candidate solutions that are transiently stored in implicit working memory. Results : We document two processes: selection of stored solutions and evolutionary search for novel solutions. During the replication of candidate solutions attractor networks occasionally produce recombinant patterns, increasing variation on which selection can act. Combinatorial search acts on multiplying units (activity patterns) with hereditary variation and novel variants appear due to (i) noisy recall of patterns from the attractor networks, (ii) noise during transmission of candidate solutions as messages between networks, and, (iii) spontaneously generated, untrained patterns in spurious attractors. Conclusions : Attractor dynamics of recurrent neural networks can be used to model Darwinian search. The proposed architecture can be used for fast search among stored solutions (by selection) and for evolutionary search when novel candidate solutions are generated in successive iterations. Since all the suggested components are present in advanced nervous systems, we hypothesize that the brain could implement a truly evolutionary combinatorial search system, capable of generating novel variants.

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

PubMed

Franks, Steven J; Kane, Nolan C; O'Hara, Niamh B; Tittes, Silas; Rest, Joshua S

2016-08-01

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome-wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late-season drought in California. These ancestor-descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (FST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome-wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Evolution of resource cycling in ecosystems and individuals.

PubMed

Crombach, Anton; Hogeweg, Paulien

2009-06-01

Resource cycling is a defining process in the maintenance of the biosphere. Microbial communities, ranging from simple to highly diverse, play a crucial role in this process. Yet the evolutionary adaptation and speciation of micro-organisms have rarely been studied in the context of resource cycling. In this study, our basic questions are how does a community evolve its resource usage and how are resource cycles partitioned? We design a computational model in which a population of individuals evolves to take up nutrients and excrete waste. The waste of one individual is another's resource. Given a fixed amount of resources, this leads to resource cycles. We find that the shortest cycle dominates the ecological dynamics, and over evolutionary time its length is minimized. Initially a single lineage processes a long cycle of resources, later crossfeeding lineages arise. The evolutionary dynamics that follow are determined by the strength of indirect selection for resource cycling. We study indirect selection by changing the spatial setting and the strength of direct selection. If individuals are fixed at lattice sites or direct selection is low, indirect selection result in lineages that structure their local environment, leading to 'smart' individuals and stable patterns of resource dynamics. The individuals are good at cycling resources themselves and do this with a short cycle. On the other hand, if individuals randomly change position each time step, or direct selection is high, individuals are more prone to crossfeeding: an ecosystem based solution with turbulent resource dynamics, and individuals that are less capable of cycling resources themselves. In a baseline model of ecosystem evolution we demonstrate different eco-evolutionary trajectories of resource cycling. By varying the strength of indirect selection through the spatial setting and direct selection, the integration of information by the evolutionary process leads to qualitatively different results from individual smartness to cooperative community structures.

The genetic architecture of normal variation in human pigmentation: an evolutionary perspective and model.

PubMed

McEvoy, Brian; Beleza, Sandra; Shriver, Mark D

2006-10-15

Skin pigmentation varies substantially across human populations in a manner largely coincident with ultraviolet radiation intensity. This observation suggests that natural selection in response to sunlight is a major force in accounting for pigmentation variability. We review recent progress in identifying the genes controlling this variation with a particular focus on the trait's evolutionary past and the potential role of testing for signatures of selection in aiding the discovery of functionally important genes. We have analyzed SNP data from the International HapMap project in 77 pigmentation candidate genes for such signatures. On the basis of these results and other similar work, we provide a tentative three-population model (West Africa, East Asia and North Europe) of the evolutionary-genetic architecture of human pigmentation. These results suggest a complex evolutionary history, with selection acting on different gene targets at different times and places in the human past. Some candidate genes may have been selected in the ancestral human population, others in the 'out of Africa' proto European-Asian population, whereas most appear to have selectively evolved solely in either Europeans or East Asians separately despite the pigmentation similarities between these two populations. Selection signatures can provide important clues to aid gene discovery. However, these should be viewed as complements, rather than replacements of, functional studies including linkage and association analyses, which can directly refine our understanding of the trait.

Evolution of dispersal in spatially and temporally variable environments: The importance of life cycles.

PubMed

Massol, François; Débarre, Florence

2015-07-01

Spatiotemporal variability of the environment is bound to affect the evolution of dispersal, and yet model predictions strongly differ on this particular effect. Recent studies on the evolution of local adaptation have shown that the life cycle chosen to model the selective effects of spatiotemporal variability of the environment is a critical factor determining evolutionary outcomes. Here, we investigate the effect of the order of events in the life cycle on the evolution of unconditional dispersal in a spatially heterogeneous, temporally varying landscape. Our results show that the occurrence of intermediate singular strategies and disruptive selection are conditioned by the temporal autocorrelation of the environment and by the life cycle. Life cycles with dispersal of adults versus dispersal of juveniles, local versus global density regulation, give radically different evolutionary outcomes that include selection for total philopatry, evolutionary bistability, selection for intermediate stable states, and evolutionary branching points. Our results highlight the importance of accounting for life-cycle specifics when predicting the effects of the environment on evolutionarily selected trait values, such as dispersal, as well as the need to check the robustness of model conclusions against modifications of the life cycle. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Genetic evolution, plasticity, and bet-hedging as adaptive responses to temporally autocorrelated fluctuating selection: A quantitative genetic model.

PubMed

Tufto, Jarle

2015-08-01

Adaptive responses to autocorrelated environmental fluctuations through evolution in mean reaction norm elevation and slope and an independent component of the phenotypic variance are analyzed using a quantitative genetic model. Analytic approximations expressing the mutual dependencies between all three response modes are derived and solved for the joint evolutionary outcome. Both genetic evolution in reaction norm elevation and plasticity are favored by slow temporal fluctuations, with plasticity, in the absence of microenvironmental variability, being the dominant evolutionary outcome for reasonable parameter values. For fast fluctuations, tracking of the optimal phenotype through genetic evolution and plasticity is limited. If residual fluctuations in the optimal phenotype are large and stabilizing selection is strong, selection then acts to increase the phenotypic variance (bet-hedging adaptive). Otherwise, canalizing selection occurs. If the phenotypic variance increases with plasticity through the effect of microenvironmental variability, this shifts the joint evolutionary balance away from plasticity in favor of genetic evolution. If microenvironmental deviations experienced by each individual at the time of development and selection are correlated, however, more plasticity evolves. The adaptive significance of evolutionary fluctuations in plasticity and the phenotypic variance, transient evolution, and the validity of the analytic approximations are investigated using simulations. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

The REH theory of protein and nucleic acid divergence - A retrospective update. [Random Evolutionary Hits

NASA Technical Reports Server (NTRS)

Holmquist, R.

1978-01-01

The random evolutionary hits (REH) theory of evolutionary divergence, originally proposed in 1972, is restated with attention to certain aspects of the theory that have caused confusion. The theory assumes that natural selection and stochastic processes interact and that natural selection restricts those codon sites which may fix mutations. The predicted total number of fixed nucleotide replacements agrees with data for cytochrome c, a-hemoglobin, beta-hemoglobin, and myoglobin. The restatement analyzes the magnitude of possible sources of errors and simplifies calculational methodology by supplying polynomial expressions to replace tables and graphs.

Darwin, artificial selection, and poverty.

PubMed

Sanchez, Luis

2010-03-01

This paper argues that the processes of evolutionary selection are becoming increasingly artificial, a trend that goes against the belief in a purely natural selection process claimed by Darwin's natural selection theory. Artificial selection is mentioned by Darwin, but it was ignored by Social Darwinists, and it is all but absent in neo-Darwinian thinking. This omission results in an underestimation of probable impacts of artificial selection upon assumed evolutionary processes, and has implications for the ideological uses of Darwin's language, particularly in relation to poverty and other social inequalities. The influence of artificial selection on genotypic and phenotypic adaptations arguably represents a substantial shift in the presumed path of evolution, a shift laden with both biological and political implications.

Evolutionary change and phylogenetic relationships in light of horizontal gene transfer.

PubMed

Boto, Luis

2015-06-01

Horizontal gene transfer has, over the past 25 years, become a part of evolutionary thinking. In the present paper I discuss horizontal gene transfer (HGT) in relation to contingency, natural selection, evolutionary change speed and the Tree-of-Life endeavour, with the aim of contributing to the understanding of the role of HGT in evolutionary processes. In addition, the challenges that HGT imposes on the current view of evolution are emphasized.

A variational approach to niche construction.

PubMed

Constant, Axel; Ramstead, Maxwell J D; Veissière, Samuel P L; Campbell, John O; Friston, Karl J

2018-04-01

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields. © 2018 The Authors.

A variational approach to niche construction

PubMed Central

Ramstead, Maxwell J. D.; Veissière, Samuel P. L.; Campbell, John O.; Friston, Karl J.

2018-01-01

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields. PMID:29643221

Eco-Evolutionary Genomics of Chromosomal Inversions.

PubMed

Wellenreuther, Maren; Bernatchez, Louis

2018-05-03

Chromosomal inversions have long fascinated evolutionary biologists due to their suppression of recombination, which can protect co-adapted alleles. Emerging research documents that inversions are commonly linked to spectacular phenotypes and have a pervasive role in eco-evolutionary processes, from mating systems, social organisation, environmental adaptation, and reproductive isolation to speciation. Studies also reveal that inversions are taxonomically widespread, with many being old and large, and that balancing selection is commonly facilitating their maintenance. This challenges the traditional view that the role of balancing selection in maintaining variation is relatively minor. The ubiquitous importance of inversions in ecological and evolutionary processes suggests that structural variation should be better acknowledged and integrated in studies pertaining to the molecular basis of adaptation and speciation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantifying evolutionary dynamics from variant-frequency time series

NASA Astrophysics Data System (ADS)

Khatri, Bhavin S.

2016-09-01

From Kimura’s neutral theory of protein evolution to Hubbell’s neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher’s angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.

Quantifying evolutionary dynamics from variant-frequency time series.

PubMed

Khatri, Bhavin S

2016-09-12

From Kimura's neutral theory of protein evolution to Hubbell's neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher's angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.

Quantitative genetic models of sexual conflict based on interacting phenotypes.

PubMed

Moore, Allen J; Pizzari, Tommaso

2005-05-01

Evolutionary conflict arises between reproductive partners when alternative reproductive opportunities are available. Sexual conflict can generate sexually antagonistic selection, which mediates sexual selection and intersexual coevolution. However, despite intense interest, the evolutionary implications of sexual conflict remain unresolved. We propose a novel theoretical approach to study the evolution of sexually antagonistic phenotypes based on quantitative genetics and the measure of social selection arising from male-female interactions. We consider the phenotype of one sex as both a genetically influenced evolving trait as well as the (evolving) social environment in which the phenotype of the opposite sex evolves. Several important points emerge from our analysis, including the relationship between direct selection on one sex and indirect effects through selection on the opposite sex. We suggest that the proposed approach may be a valuable tool to complement other theoretical approaches currently used to study sexual conflict. Most importantly, our approach highlights areas where additional empirical data can help clarify the role of sexual conflict in the evolutionary process.

Comparative phylogenetic analysis of male alternative reproductive tactics in ray-finned fishes.

PubMed

Mank, Judith E; Avise, John C

2006-06-01

Using comparative phylogenetic analysis, we analyzed the evolution of male alternative reproductive tactics (MARTs) in ray-finned fishes (Actinopterygii). Numerous independent origins for each type of MART (involving sneaker males, female mimics, pirates, and satellite males) indicate that these behaviors have been highly labile across actinopterygiian evolution, consistent with a previous notion that convergent selection in fishes can readily mold the underlying suites of reproductive hormones into similar behaviors. The evolutionary appearance of MARTs was significantly correlated with the presence of sexually selected traits in bourgeois males (P = 0.001) but not with the presence of male parental care. This suggests that MARTs often arise from selection on some males to circumvent bourgeois male investment in mate monopolization, rather than to avoid male brood care per se. We found parsimony evidence for an evolutionary progression of MARTs wherein sneaking is usually the evolutionary precursor to the presumably more complex MARTs of female mimicry and cooperative satellite behavior. Nest piracy appears not to be part of this evolutionary progression, possibly because its late onset in the life cycle of most ray-finned fishes reduces the effects of selection on this reproductive tactic.

Expanding the eco-evolutionary context of herbicide resistance research.

PubMed

Neve, Paul; Busi, Roberto; Renton, Michael; Vila-Aiub, Martin M

2014-09-01

The potential for human-driven evolution in economically and environmentally important organisms in medicine, agriculture and conservation management is now widely recognised. The evolution of herbicide resistance in weeds is a classic example of rapid adaptation in the face of human-mediated selection. Management strategies that aim to slow or prevent the evolution of herbicide resistance must be informed by an understanding of the ecological and evolutionary factors that drive selection in weed populations. Here, we argue for a greater focus on the ultimate causes of selection for resistance in herbicide resistance studies. The emerging fields of eco-evolutionary dynamics and applied evolutionary biology offer a means to achieve this goal and to consider herbicide resistance in a broader and sometimes novel context. Four relevant research questions are presented, which examine (i) the impact of herbicide dose on selection for resistance, (ii) plant fitness in herbicide resistance studies, (iii) the efficacy of herbicide rotations and mixtures and (iv) the impacts of gene flow on resistance evolution and spread. In all cases, fundamental ecology and evolution have the potential to offer new insights into herbicide resistance evolution and management. © 2014 Society of Chemical Industry.

Chaos and unpredictability in evolution.

PubMed

Doebeli, Michael; Ispolatov, Iaroslav

2014-05-01

The possibility of complicated dynamic behavior driven by nonlinear feedbacks in dynamical systems has revolutionized science in the latter part of the last century. Yet despite examples of complicated frequency dynamics, the possibility of long-term evolutionary chaos is rarely considered. The concept of "survival of the fittest" is central to much evolutionary thinking and embodies a perspective of evolution as a directional optimization process exhibiting simple, predictable dynamics. This perspective is adequate for simple scenarios, when frequency-independent selection acts on scalar phenotypes. However, in most organisms many phenotypic properties combine in complicated ways to determine ecological interactions, and hence frequency-dependent selection. Therefore, it is natural to consider models for evolutionary dynamics generated by frequency-dependent selection acting simultaneously on many different phenotypes. Here we show that complicated, chaotic dynamics of long-term evolutionary trajectories in phenotype space is very common in a large class of such models when the dimension of phenotype space is large, and when there are selective interactions between the phenotypic components. Our results suggest that the perspective of evolution as a process with simple, predictable dynamics covers only a small fragment of long-term evolution. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

The evolutionary legacy of size-selective harvesting extends from genes to populations

PubMed Central

Uusi-Heikkilä, Silva; Whiteley, Andrew R; Kuparinen, Anna; Matsumura, Shuichi; Venturelli, Paul A; Wolter, Christian; Slate, Jon; Primmer, Craig R; Meinelt, Thomas; Killen, Shaun S; Bierbach, David; Polverino, Giovanni; Ludwig, Arne; Arlinghaus, Robert

2015-01-01

Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of wild-origin zebrafish (Danio rerio). Fish adapted to high positively size selective fishing pressure invested more in reproduction, reached a smaller adult body size, and were less explorative and bold. Phenotypic changes seemed subtle but were accompanied by genetic changes in functional loci. Thus, our results provided unambiguous evidence for rapid, harvest-induced phenotypic and evolutionary change when harvesting is intensive and size selective. According to a life-history model, the observed life-history changes elevated population growth rate in harvested conditions, but slowed population recovery under a simulated moratorium. Hence, the evolutionary legacy of size-selective harvesting includes populations that are productive under exploited conditions, but selectively disadvantaged to cope with natural selection pressures that often favor large body size. PMID:26136825

Does selection on increased cold tolerance in the adult stage confer resistance throughout development?

PubMed

Dierks, A; Kölzow, N; Franke, K; Fischer, K

2012-08-01

Artificial selection is a powerful approach to unravel constraints on genetic adaptation. Although it has been frequently used to reveal genetic trade-offs among different fitness-related traits, only a few studies have targeted genetic correlations across developmental stages. Here, we test whether selection on increased cold tolerance in the adult stage increases cold resistance throughout ontogeny in the butterfly Bicyclus anynana. We used lines selected for decreased chill-coma recovery time and corresponding controls, which had originally been set up from three levels of inbreeding (outbred control, one or two full-sib matings). Four generations after having terminated selection, a response to selection was found in 1-day-old butterflies (the age at which selection took place). Older adults showed a very similar although weaker response. Nevertheless, cold resistance did not increase in either egg, larval or pupal stage in the selection lines but was even lower compared to control lines for eggs and young larvae. These findings suggest a cost of increased adult cold tolerance, presumably reducing resource availability for offspring provisioning and thereby stress tolerance during development, which may substantially affect evolutionary trajectories. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes.

PubMed

Lin, Chieh-Hua; Lian, Chun-Yi; Hsiung, Chao Agnes; Chen, Feng-Chi

2011-10-05

Changes in transcriptional orientation ("CTOs") occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication and transcription and an increase in mutation rate. However, CTOs do not always lead to the replication-transcription confrontation. Furthermore, CTOs may cause deleterious disruptions of operon structure and/or gene regulations. The currently existing CTOs may indicate relaxation of selection pressure. Therefore, it is of interest to investigate whether CTOs have an independent effect on the evolutionary rates of the affected genes, and whether these genes are subject to any type of selection pressure in prokaryotes. Three closely related enterbacteria, Escherichia coli, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium, were selected for comparisons of synonymous (dS) and nonsynonymous (dN) substitution rate between the genes that have experienced changes in transcriptional orientation (changed-orientation genes, "COGs") and those that do not (same-orientation genes, "SOGs"). The dN/dS ratio was also derived to evaluate the selection pressure on the analyzed genes. Confounding factors in the estimation of evolutionary rates, such as gene essentiality, gene expression level, replication-transcription confrontation, and decreased dS at gene terminals were controlled in the COG-SOG comparisons. We demonstrate that COGs have significantly higher dN and dS than SOGs when a series of confounding factors are controlled. However, the dN/dS ratios are similar between the two gene groups, suggesting that the increase in dS can sufficiently explain the increase in dN in COGs. Therefore, the increases in evolutionary rates in COGs may be mainly mutation-driven. Here we show that CTOs can increase the evolutionary rates of the affected genes. This effect is independent of the replication-transcription confrontation, which is suggested to be the major cause of inversion-associated evolutionary rate increases. The real cause of such evolutionary rate increases remains unclear but is worth further explorations.

The tale of the shrinking weapon: seasonal changes in nutrition affect weapon size and sexual dimorphism, but not contemporary evolution.

PubMed

Miller, C W; McDonald, G C; Moore, A J

2016-11-01

Sexually selected traits are often highly variable in size within populations due to their close link with the physical condition of individuals. Nutrition has a large impact on physical condition, and thus, any seasonal changes in nutritional quality are predicted to alter the average size of sexually selected traits as well as the degree of sexual dimorphism in populations. However, although traits affected by mate choice are well studied, we have a surprising lack of knowledge of how natural variation in nutrition affects the expression of sexually selected weapons and sexual dimorphism. Further, few studies explicitly test for differences in the heritability and mean-scaled evolvability of sexually selected traits across conditions. We studied Narnia femorata (Hemiptera: Coreidae), an insect where males use their hind legs as weapons and the femurs are enlarged, to understand the extent to which weapon expression, sexual dimorphism and evolvability change across the actual range of nutrition available in the wild. We found that insects raised on a poor diet (cactus without fruit) are nearly monomorphic, whereas those raised on a high-quality diet (cactus with ripe fruit) are distinctly sexually dimorphic via the expression of large hind leg weapons in males. Contrary to our expectations, we found little evidence of a potential for evolutionary change for any trait measured. Thus, although we show weapons are highly condition dependent, and changes in weapon expression and dimorphism could alter evolutionary dynamics, our populations are unlikely to experience further evolutionary changes under current conditions. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Squamate hatchling size and the evolutionary causes of negative offspring size allometry.

PubMed

Meiri, S; Feldman, A; Kratochvíl, L

2015-02-01

Although fecundity selection is ubiquitous, in an overwhelming majority of animal lineages, small species produce smaller number of offspring per clutch. In this context, egg, hatchling and neonate sizes are absolutely larger, but smaller relative to adult body size in larger species. The evolutionary causes of this widespread phenomenon are not fully explored. The negative offspring size allometry can result from processes limiting maximal egg/offspring size forcing larger species to produce relatively smaller offspring ('upper limit'), or from a limit on minimal egg/offspring size forcing smaller species to produce relatively larger offspring ('lower limit'). Several reptile lineages have invariant clutch sizes, where females always lay either one or two eggs per clutch. These lineages offer an interesting perspective on the general evolutionary forces driving negative offspring size allometry, because an important selective factor, fecundity selection in a single clutch, is eliminated here. Under the upper limit hypotheses, large offspring should be selected against in lineages with invariant clutch sizes as well, and these lineages should therefore exhibit the same, or shallower, offspring size allometry as lineages with variable clutch size. On the other hand, the lower limit hypotheses would allow lineages with invariant clutch sizes to have steeper offspring size allometries. Using an extensive data set on the hatchling and female sizes of > 1800 species of squamates, we document that negative offspring size allometry is widespread in lizards and snakes with variable clutch sizes and that some lineages with invariant clutch sizes have unusually steep offspring size allometries. These findings suggest that the negative offspring size allometry is driven by a constraint on minimal offspring size, which scales with a negative allometry. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles.

PubMed

Orozco-terWengel, Pablo; Kapun, Martin; Nolte, Viola; Kofler, Robert; Flatt, Thomas; Schlötterer, Christian

2012-10-01

The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome-wide next generation sequencing of DNA pools (Pool-Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a pronounced genomic response to selection, with almost 5000 single nucleotide polymorphisms (SNP; genome-wide false discovery rates < 0.005%) deviating from neutral expectation. Importantly, the evolutionary trajectories of the selected alleles were heterogeneous, with the alleles falling into two distinct classes: (i) alleles that continuously rise in frequency; and (ii) alleles that at first increase rapidly but whose frequencies then reach a plateau. Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects. © 2012 Blackwell Publishing Ltd.

Mirages and the nature of Pluto's atmosphere

NASA Technical Reports Server (NTRS)

Stansberry, J. A.; Lunine, J. I.; Hubbard, W. B.; Yelle, R. V.; Hunten, D. M.

1994-01-01

We present model occultation lightcurves demonstrating that a strong thermal inversion layer at the base of Pluto's stratosphere can reproduce the minimum flux measured by the Kuiper Airborne Observatory (KAO) during the 1988 occultation of a star by Pluto. The inversion layer also forms the occultation equivalent of a mirage at a radius of 1198 km, which is capable of hiding tropospheres of significant depth. Pluto's surface lies below 1198 km, its radius depending on the depth of the troposphere. We begin by computing plausible temperature structures for Pluto's lower atmosphere, constrained by a calculation of the temperature of the atmosphere near the surface. We then trace rays from the occulted star through the model atmosphere, computing the resultant bending of the ray. Model light curves are obtained by summing the contribution of individual rays within the shadow of Pluto on Earth. We find that we can reproduce the KAO lightcurve using model atmospheres with a temperature inversion and no haze. We have explored models with tropospheres as deep as 40 km (implying a Pluto radius of 1158 km) that reproduce the suite of occultation data. Deeper tropospheres can be fitted to the data, but the mutual event radius of 1150 km probably provides a lower bound. If Pluto has a shallow or nonexistent troposphere, its density is consistent with formation in the solar nebula with modest water loss due to impact ejection. If the troposhere is relatively deep, implying a smaller radius and larger density, significant amounts of water loss are required.

JCoDA: a tool for detecting evolutionary selection.

PubMed

Steinway, Steven N; Dannenfelser, Ruth; Laucius, Christopher D; Hayes, James E; Nayak, Sudhir

2010-05-27

The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway. JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda.

JCoDA: a tool for detecting evolutionary selection

PubMed Central

2010-01-01

Background The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. Results JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway. Conclusions JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda. PMID:20507581

Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

PubMed Central

2011-01-01

Background Several susceptibility genetic variants for autoimmune diseases have been identified. A subset of these polymorphisms displays an opposite risk profile in different autoimmune conditions. This observation open interesting questions on the evolutionary forces shaping the frequency of these alleles in human populations. We aimed at testing the hypothesis whereby balancing selection has shaped the frequency of opposite risk alleles. Results Since balancing selection signatures are expected to extend over short genomic portions, we focused our analyses on 11 regions carrying putative functional polymorphisms that may represent the disease variants (and the selection targets). No exceptional nucleotide diversity was observed for ZSCAN23, HLA-DMB, VARS2, PTPN22, BAT3, C6orf47, and IL10; summary statistics were consistent with evolutionary neutrality for these gene regions. Conversely, CDSN/PSORS1C1, TRIM10/TRIM40, BTNL2, and TAP2 showed extremely high nucleotide diversity and most tests rejected neutrality, suggesting the action of balancing selection. For TAP2 and BTNL2 these signatures are not secondary to linkage disequilibrium with HLA class II genes. Nonetheless, with the exception of variants in TRIM40 and CDSN, our data suggest that opposite risk SNPs are not selection targets but rather have accumulated as neutral variants. Conclusion Data herein indicate that balancing selection is common within the extended MHC region and involves several non-HLA loci. Yet, the evolutionary history of most SNPs with an opposite effect for autoimmune diseases is consistent with evolutionary neutrality. We suggest that variants with an opposite effect on autoimmune diseases should not be considered a distinct class of disease alleles from the evolutionary perspective and, in a few cases, the opposite effect on distinct diseases may derive from complex haplotype structures in regions with high genetic diversity. PMID:21682861

Promotion of cooperation by selective group extinction

NASA Astrophysics Data System (ADS)

Böttcher, Marvin A.; Nagler, Jan

2016-06-01

Multilevel selection is an important organizing principle that crucially underlies evolutionary processes from the emergence of cells to eusociality and the economics of nations. Previous studies on multilevel selection assumed that the effective higher-level selection emerges from lower-level reproduction. This leads to selection among groups, although only individuals reproduce. We introduce selective group extinction, where groups die with a probability inversely proportional to their group fitness. When accounting for this the critical benefit-to-cost ratio is substantially lowered. Because in game theory and evolutionary dynamics the degree of cooperation crucially depends on this ratio above which cooperation emerges, previous studies may have substantially underestimated the establishment and maintenance of cooperation.

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

PubMed Central

Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

2011-01-01

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

Relative importance of evolutionary dynamics depends on the composition of microbial predator-prey community.

PubMed

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-06-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities.

Relative importance of evolutionary dynamics depends on the composition of microbial predator–prey community

PubMed Central

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-01-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities. PMID:26684728

Experimental evolution reveals differences between phenotypic and evolutionary responses to population density.

PubMed

McNamara, K B; Simmons, L W

2017-09-01

Group living can select for increased immunity, given the heightened risk of parasite transmission. Yet, it also may select for increased male reproductive investment, given the elevated risk of female multiple mating. Trade-offs between immunity and reproduction are well documented. Phenotypically, population density mediates both reproductive investment and immune function in the Indian meal moth, Plodia interpunctella. However, the evolutionary response of populations to these traits is unknown. We created two replicated populations of P. interpunctella, reared and mated for 14 generations under high or low population densities. These population densities cause plastic responses in immunity and reproduction: at higher numbers, both sexes invest more in one index of immunity [phenoloxidase (PO) activity] and males invest more in sperm. Interestingly, our data revealed divergence in PO and reproduction in a different direction to previously reported phenotypic responses. Males evolving at low population densities transferred more sperm, and both males and females displayed higher PO than individuals at high population densities. These positively correlated responses to selection suggest no apparent evolutionary trade-off between immunity and reproduction. We speculate that the reduced PO activity and sperm investment when evolving under high population density may be due to the reduced population fitness predicted under increased sexual conflict and/or to trade-offs between pre- and post-copulatory traits. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Differences in evolutionary pressure acting within highly conserved ortholog groups.

PubMed

Przytycka, Teresa M; Jothi, Raja; Aravind, L; Lipman, David J

2008-07-17

In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions. Using a set of ortholog groups from prokaryotes, with a single representative in each studied organism, we asked the question if this evolutionary pressure is acting similarly on different subgroups of orthologs defined as major lineages (e.g. Proteobacteria or Firmicutes). Using correlations in entropy measures as a proxy for evolutionary pressure, we observed two distinct behaviors within our ortholog collection. The first subset of ortholog groups, called here informational, consisted mostly of proteins associated with information processing (i.e. translation, transcription, DNA replication) and the second, the non-informational ortholog groups, mostly comprised of proteins involved in metabolic pathways. The evolutionary pressure acting on non-informational proteins is more uniform relative to their informational counterparts. The non-informational proteins show higher level of correlation between entropy profiles and more uniformity across subgroups. The low correlation of entropy profiles in the informational ortholog groups suggest that the evolutionary pressure acting on the informational ortholog groups is not uniform across different clades considered this study. This might suggest "fine-tuning" of informational proteins in each lineage leading to lineage-specific differences in selection. This, in turn, could make these proteins less exchangeable between lineages. In contrast, the uniformity of the selective pressure acting on the non-informational groups might allow the exchange of the genetic material via lateral gene transfer.

Evolutionary Agroecology: the potential for cooperative, high density, weed-suppressing cereals.

PubMed

Weiner, Jacob; Andersen, Sven B; Wille, Wibke K-M; Griepentrog, Hans W; Olsen, Jannie M

2010-09-01

Evolutionary theory can be applied to improve agricultural yields and/or sustainability, an approach we call Evolutionary Agroecology. The basic idea is that plant breeding is unlikely to improve attributes already favored by millions of years of natural selection, whereas there may be unutilized potential in selecting for attributes that increase total crop yield but reduce plants' individual fitness. In other words, plant breeding should be based on group selection. We explore this approach in relation to crop-weed competition, and argue that it should be possible to develop high density cereals that can utilize their initial size advantage over weeds to suppress them much better than under current practices, thus reducing or eliminating the need for chemical or mechanical weed control. We emphasize the role of density in applying group selection to crops: it is competition among individuals that generates the 'Tragedy of the Commons', providing opportunities to improve plant production by selecting for attributes that natural selection would not favor. When there is competition for light, natural selection of individuals favors a defensive strategy of 'shade avoidance', but a collective, offensive 'shading' strategy could increase weed suppression and yield in the high density, high uniformity cropping systems we envision.

Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry.

PubMed

Schott, Ryan K; Van Nynatten, Alexander; Card, Daren C; Castoe, Todd A; S W Chang, Belinda

2018-06-01

The visual systems of snakes are heavily modified relative to other squamates, a condition often thought to reflect their fossorial origins. Further modifications are seen in caenophidian snakes, where evolutionary transitions between rod and cone photoreceptors, termed photoreceptor transmutations, have occurred in many lineages. Little previous work, however, has focused on the molecular evolutionary underpinnings of these morphological changes. To address this, we sequenced seven snake eye transcriptomes and utilized new whole-genome and targeted capture sequencing data. We used these data to analyze gene loss and shifts in selection pressures in phototransduction genes that may be associated with snake evolutionary origins and photoreceptor transmutation. We identified the surprising loss of rhodopsin kinase (GRK1), despite a low degree of gene loss overall and a lack of relaxed selection early during snake evolution. These results provide some of the first evolutionary genomic corroboration for a dim-light ancestor that lacks strong fossorial adaptations. Our results also indicate that snakes with photoreceptor transmutation experienced significantly different selection pressures from other reptiles. Significant positive selection was found primarily in cone-specific genes, but not rod-specific genes, contrary to our expectations. These results reveal potential molecular adaptations associated with photoreceptor transmutation and also highlight unappreciated functional differences between rod- and cone-specific phototransduction proteins. This intriguing example of snake visual system evolution illustrates how the underlying molecular components of a complex system can be reshaped in response to changing selection pressures.

Phylogenetic Paleoecology: Tree-Thinking and Ecology in Deep Time.

PubMed

Lamsdell, James C; Congreve, Curtis R; Hopkins, Melanie J; Krug, Andrew Z; Patzkowsky, Mark E

2017-06-01

The new and emerging field of phylogenetic paleoecology leverages the evolutionary relationships among species to explain temporal and spatial changes in species diversity, abundance, and distribution in deep time. This field is poised for rapid progress as knowledge of the evolutionary relationships among fossil species continues to expand. In particular, this approach will lend new insights to many of the longstanding questions in evolutionary biology, such as: the relationships among character change, ecology, and evolutionary rates; the processes that determine the evolutionary relationships among species within communities and along environmental gradients; and the phylogenetic signal underlying ecological selectivity in background and mass extinctions and in major evolutionary radiations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolution of a predator-induced, nonlinear reaction norm.

PubMed

Carter, Mauricio J; Lind, Martin I; Dennis, Stuart R; Hentley, William; Beckerman, Andrew P

2017-08-30

Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory suggests contrasting micro-evolutionary responses to selection. Daphnia pulex is an ideal species to explore the micro-evolutionary response of anti-predator traits because they face heterogeneous predation regimes, sometimes experiencing only invertebrate midge predators and other times experiencing vertebrate fish and invertebrate midge predators. We explored plausible patterns of adaptive evolution of a predator-induced morphological reaction norm. We combined estimates of selection gradients that characterize the various habitats that D. pulex experiences with detail on the quantitative genetic architecture of inducible morphological defences. Our data reveal a fine scale description of daphnid defensive reaction norms, and a strong covariance between the sensitivity to cues and the maximum response to cues. By analysing the response of the reaction norm to plausible, predator-specific selection gradients, we show how in the context of this covariance, micro-evolution may be more uniform than predicted from size-selective predation theory. Our results show how covariance between the sensitivity to cues and the maximum response to cues for morphological defence can shape the evolutionary trajectory of predator-induced defences in D. pulex . © 2017 The Authors.

The Current Status of the Philosophy of Biology

NASA Astrophysics Data System (ADS)

Takacs, Peter; Ruse, Michael

2013-01-01

The philosophy of biology today is one of the most exciting areas of philosophy. It looks critically across the life sciences, teasing out conceptual issues and difficulties bringing to bear the tools of philosophical analysis to achieve clarification and understanding. This essay surveys work in all of the major directions of research: evolutionary theory and the units/levels of selection; evolutionary developmental biology; reductionism; ecology; the species problem; teleology; evolutionary epistemology; evolutionary ethics; and progress. There is a comprehensive bibliography.

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.

Evolutionary dynamics of the leaf phenological cycle in an oak metapopulation along an elevation gradient.

PubMed

Firmat, C; Delzon, S; Louvet, J-M; Parmentier, J; Kremer, A

2017-12-01

It has been predicted that environmental changes will radically alter the selective pressures on phenological traits. Long-lived species, such as trees, will be particularly affected, as they may need to undergo major adaptive change over only one or a few generations. The traits describing the annual life cycle of trees are generally highly evolvable, but nothing is known about the strength of their genetic correlations. Tight correlations can impose strong evolutionary constraints, potentially hampering the adaptation of multivariate phenological phenotypes. In this study, we investigated the evolutionary, genetic and environmental components of the timing of leaf unfolding and senescence within an oak metapopulation along an elevation gradient. Population divergence, estimated from in situ and common-garden data, was compared to expectations under neutral evolution, based on microsatellite markers. This approach made it possible (1) to evaluate the influence of genetic correlation on multivariate local adaptation to elevation and (2) to identify traits probably exposed to past selective pressures due to the colder climate at high elevation. The genetic correlation was positive but very weak, indicating that genetic constraints did not shape the local adaptation pattern for leaf phenology. Both spring and fall (leaf unfolding and senescence, respectively) phenology timings were involved in local adaptation, but leaf unfolding was probably the trait most exposed to climate change-induced selection. Our data indicated that genetic variation makes a much smaller contribution to adaptation than the considerable plastic variation displayed by a tree during its lifetime. The evolutionary potential of leaf phenology is, therefore, probably not the most critical aspect for short-term population survival in a changing climate. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

What to expect from an evolutionary hypothesis for a human disease: The case of type 2 diabetes.

PubMed

Watve, Milind; Diwekar-Joshi, Manawa

2016-10-01

Evolutionary medicine has a promise to bring in a conceptual revolution in medicine. However, as yet the field does not have the same theoretical rigour as that of many other fields in evolutionary studies. We discuss here with reference to type 2 diabetes mellitus (T2DM) what role an evolutionary hypothesis should play in the development of thinking in medicine. Starting with the thrifty gene hypothesis, evolutionary thinking in T2DM has undergone several transitions, modifications and refinements of the thrift family of hypotheses. In addition alternative hypotheses independent of thrift are also suggested. However, most hypotheses look at partial pictures; make selective use of supportive data ignoring inconvenient truths. Most hypotheses look at a superficial picture and avoid getting into the intricacies of underlying molecular, neuronal and physiological processes. Very few hypotheses have suggested clinical implications and none of them have been tested with randomized clinical trials. In the meanwhile the concepts in the pathophysiology of T2DM are undergoing radical changes and evolutionary hypotheses need to take them into account. We suggest an approach and a set of criteria to evaluate the relative merits of the alternative hypotheses. A number of hypotheses are likely to fail when critically evaluated against these criteria. It is possible that more than one selective process are at work in the evolution of propensity to T2DM, but the intercompatibility of the alternative selective forces and their relative contribution needs to be examined. The approach we describe could potentially lead to a sound evolutionary theory that is clinically useful and testable by randomized controlled clinical trials. Copyright © 2016 Elsevier GmbH. All rights reserved.

On Reciprocal Causation in the Evolutionary Process.

PubMed

Svensson, Erik I

2018-01-01

Recent calls for a revision of standard evolutionary theory (SET) are based partly on arguments about the reciprocal causation. Reciprocal causation means that cause-effect relationships are bi-directional, as a cause could later become an effect and vice versa. Such dynamic cause-effect relationships raise questions about the distinction between proximate and ultimate causes, as originally formulated by Ernst Mayr. They have also motivated some biologists and philosophers to argue for an Extended Evolutionary Synthesis (EES). The EES will supposedly expand the scope of the Modern Synthesis (MS) and SET, which has been characterized as gene-centred, relying primarily on natural selection and largely neglecting reciprocal causation. Here, I critically examine these claims, with a special focus on the last conjecture. I conclude that reciprocal causation has long been recognized as important by naturalists, ecologists and evolutionary biologists working in the in the MS tradition, although it it could be explored even further. Numerous empirical examples of reciprocal causation in the form of positive and negative feedback are now well known from both natural and laboratory systems. Reciprocal causation have also been explicitly incorporated in mathematical models of coevolutionary arms races, frequency-dependent selection, eco-evolutionary dynamics and sexual selection. Such dynamic feedback were already recognized by Richard Levins and Richard Lewontin in their bok The Dialectical Biologist . Reciprocal causation and dynamic feedback might also be one of the few contributions of dialectical thinking and Marxist philosophy in evolutionary theory. I discuss some promising empirical and analytical tools to study reciprocal causation and the implications for the EES. Finally, I briefly discuss how quantitative genetics can be adapated to studies of reciprocal causation, constructive inheritance and phenotypic plasticity and suggest that the flexibility of this approach might have been underestimated by critics of contemporary evolutionary biology.

Rapid changes in genetic architecture of behavioural syndromes following colonization of a novel environment.

PubMed

Karlsson Green, K; Eroukhmanoff, F; Harris, S; Pettersson, L B; Svensson, E I

2016-01-01

Behavioural syndromes, that is correlated behaviours, may be a result from adaptive correlational selection, but in a new environmental setting, the trait correlation might act as an evolutionary constraint. However, knowledge about the quantitative genetic basis of behavioural syndromes, and the stability and evolvability of genetic correlations under different ecological conditions, is limited. We investigated the quantitative genetic basis of correlated behaviours in the freshwater isopod Asellus aquaticus. In some Swedish lakes, A. aquaticus has recently colonized a novel habitat and diverged into two ecotypes, presumably due to habitat-specific selection from predation. Using a common garden approach and animal model analyses, we estimated quantitative genetic parameters for behavioural traits and compared the genetic architecture between the ecotypes. We report that the genetic covariance structure of the behavioural traits has been altered in the novel ecotype, demonstrating divergence in behavioural correlations. Thus, our study confirms that genetic correlations behind behaviours can change rapidly in response to novel selective environments. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

The limits of weak selection and large population size in evolutionary game theory.

PubMed

Sample, Christine; Allen, Benjamin

2017-11-01

Evolutionary game theory is a mathematical approach to studying how social behaviors evolve. In many recent works, evolutionary competition between strategies is modeled as a stochastic process in a finite population. In this context, two limits are both mathematically convenient and biologically relevant: weak selection and large population size. These limits can be combined in different ways, leading to potentially different results. We consider two orderings: the [Formula: see text] limit, in which weak selection is applied before the large population limit, and the [Formula: see text] limit, in which the order is reversed. Formal mathematical definitions of the [Formula: see text] and [Formula: see text] limits are provided. Applying these definitions to the Moran process of evolutionary game theory, we obtain asymptotic expressions for fixation probability and conditions for success in these limits. We find that the asymptotic expressions for fixation probability, and the conditions for a strategy to be favored over a neutral mutation, are different in the [Formula: see text] and [Formula: see text] limits. However, the ordering of limits does not affect the conditions for one strategy to be favored over another.

Natural selection stops the evolution of male attractiveness

PubMed Central

Hine, Emma; McGuigan, Katrina; Blows, Mark W.

2011-01-01

Sexual selection in natural populations acts on highly heritable traits and tends to be relatively strong, implicating sexual selection as a causal agent in many phenotypic radiations. Sexual selection appears to be ineffectual in promoting phenotypic divergence among contemporary natural populations, however, and there is little evidence from artificial selection experiments that sexual fitness can evolve. Here, we demonstrate that a multivariate male trait preferred by Drosophila serrata females can respond to selection and results in the maintenance of male mating success. The response to selection was associated with a gene of major effect increasing in frequency from 12 to 35% in seven generations. No further response to selection, or increase in frequency of the major gene, was observed between generations 7 and 11, indicating an evolutionary limit had been reached. Genetic analyses excluded both depletion of genetic variation and overdominance as causes of the evolutionary limit. Relaxing artificial selection resulted in the loss of 52% of the selection response after a further five generations, demonstrating that the response under artificial sexual selection was opposed by antagonistic natural selection. We conclude that male D. serrata sexually selected traits, and attractiveness to D. serrata females conferred by these traits, were held at an evolutionary limit by the lack of genetic variation that would allow an increase in sexual fitness while simultaneously maintaining nonsexual fitness. Our results suggest that sexual selection is unlikely to cause divergence among natural populations without a concomitant change in natural selection, a conclusion consistent with observational evidence from natural populations. PMID:21321197

Evolutionary heritage influences Amazon tree ecology.

PubMed

Coelho de Souza, Fernanda; Dexter, Kyle G; Phillips, Oliver L; Brienen, Roel J W; Chave, Jerome; Galbraith, David R; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E O C; Araujo-Murakami, Alejandro; Arets, Eric J M M; Aymard C, Gerardo A; Baraloto, Christopher; Barroso, Jorcely G; Bonal, Damien; Boot, Rene G A; Camargo, José L C; Comiskey, James A; Valverde, Fernando Cornejo; de Camargo, Plínio B; Di Fiore, Anthony; Elias, Fernando; Erwin, Terry L; Feldpausch, Ted R; Ferreira, Leandro; Fyllas, Nikolaos M; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N; Killeen, Timothy J; Laurance, William F; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S; Marimon-Junior, Ben H; Mendoza, Casimiro; Morandi, Paulo; Neill, David A; Vargas, Percy Núñez; Oliveira, Edmar A; Lenza, Eddie; Palacios, Walter A; Peñuela-Mora, Maria C; Pipoly, John J; Pitman, Nigel C A; Prieto, Adriana; Quesada, Carlos A; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P; Silveira, Marcos; Stropp, Juliana; Ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M F; van der Meer, Peter J; Vasquez, Rodolfo V; Vieira, Simone A; Vilanova, Emilio; Vos, Vincent A; Wang, Ophelia; Young, Kenneth R; Zagt, Roderick J; Baker, Timothy R

2016-12-14

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. © 2016 The Authors.

Evolutionary genetics of maternal effects

PubMed Central

Wolf, Jason B.; Wade, Michael J.

2016-01-01

Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

Evolutionary heritage influences Amazon tree ecology

PubMed Central

Coelho de Souza, Fernanda; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J. W.; Chave, Jerome; Galbraith, David R.; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R. Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E. O. C.; Araujo-Murakami, Alejandro; Arets, Eric J. M. M.; Aymard C, Gerardo A.; Baraloto, Christopher; Barroso, Jorcely G.; Bonal, Damien; Boot, Rene G. A.; Camargo, José L. C.; Comiskey, James A.; Valverde, Fernando Cornejo; de Camargo, Plínio B.; Di Fiore, Anthony; Erwin, Terry L.; Feldpausch, Ted R.; Ferreira, Leandro; Fyllas, Nikolaos M.; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N.; Killeen, Timothy J.; Laurance, William F.; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E.; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S.; Marimon-Junior, Ben H.; Mendoza, Casimiro; Morandi, Paulo; Neill, David A.; Vargas, Percy Núñez; Oliveira, Edmar A.; Lenza, Eddie; Palacios, Walter A.; Peñuela-Mora, Maria C.; Pipoly, John J.; Pitman, Nigel C. A.; Prieto, Adriana; Quesada, Carlos A.; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P.; Silveira, Marcos; ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M. F.; van der Meer, Peter J.; Vasquez, Rodolfo V.; Vieira, Simone A.; Vilanova, Emilio; Vos, Vincent A.; Wang, Ophelia; Young, Kenneth R.; Zagt, Roderick J.; Baker, Timothy R.

2016-01-01

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. PMID:27974517

Preferential selection based on strategy persistence and memory promotes cooperation in evolutionary prisoner's dilemma games

NASA Astrophysics Data System (ADS)

Liu, Yuanming; Huang, Changwei; Dai, Qionglin

2018-06-01

Strategy imitation plays a crucial role in evolutionary dynamics when we investigate the spontaneous emergence of cooperation under the framework of evolutionary game theory. Generally, when an individual updates his strategy, he needs to choose a role model whom he will learn from. In previous studies, individuals choose role models randomly from their neighbors. In recent works, researchers have considered that individuals choose role models according to neighbors' attractiveness characterized by the present network topology or historical payoffs. Here, we associate an individual's attractiveness with the strategy persistence, which characterizes how frequently he changes his strategy. We introduce a preferential parameter α to describe the nonlinear correlation between the selection probability and the strategy persistence and the memory length of individuals M into the evolutionary games. We investigate the effects of α and M on cooperation. Our results show that cooperation could be promoted when α > 0 and at the same time M > 1, which corresponds to the situation that individuals are inclined to select their neighbors with relatively higher persistence levels during the evolution. Moreover, we find that the cooperation level could reach the maximum at an optimal memory length when α > 0. Our work sheds light on how to promote cooperation through preferential selection based on strategy persistence and a limited memory length.

Selection in a fluctuating environment and the evolution of sexual dimorphism in the seed beetle Callosobruchus maculatus.

PubMed

Hallsson, L R; Björklund, M

2012-08-01

Temperature changes in the environment, which realistically include environmental fluctuations, can create both plastic and evolutionary responses of traits. Sexes might differ in either or both of these responses for homologous traits, which in turn has consequences for sexual dimorphism and its evolution. Here, we investigate both immediate changes in and the evolution of sexual dimorphism in response to a changing environment (with and without fluctuations) using the seed beetle Callosobruchus maculatus. We investigate sex differences in plasticity and also the genetic architecture of body mass and developmental time dimorphism to test two existing hypotheses on sex differences in plasticity (adaptive canalization hypothesis and condition dependence hypothesis). We found a decreased sexual size dimorphism in higher temperature and that females responded more plastically than males, supporting the condition dependence hypothesis. However, selection in a fluctuating environment altered sex-specific patterns of genetic and environmental variation, indicating support for the adaptive canalization hypothesis. Genetic correlations between sexes (r(MF) ) were affected by fluctuating selection, suggesting facilitated independent evolution of the sexes. Thus, the selective past of a population is highly important for the understanding of the evolutionary dynamics of sexual dimorphism. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

The σ law of evolutionary dynamics in community-structured population.

PubMed

Tang, Changbing; Li, Xiang; Cao, Lang; Zhan, Jingyuan

2012-08-07

Evolutionary game dynamics in finite populations provide a new framework to understand the selection of traits with frequency-dependent fitness. Recently, a simple but fundamental law of evolutionary dynamics, which we call σ law, describes how to determine the selection between two competing strategies: in most evolutionary processes with two strategies, A and B, strategy A is favored over B in weak selection if and only if σR+S>T+σP. This relationship holds for a wide variety of structured populations with mutation rate and weak selection under certain assumptions. In this paper, we propose a model of games based on a community-structured population and revisit this law under the Moran process. By calculating the average payoffs of A and B individuals with the method of effective sojourn time, we find that σ features not only the structured population characteristics, but also the reaction rate between individuals. That is to say, an interaction between two individuals are not uniform, and we can take σ as a reaction rate between any two individuals with the same strategy. We verify this viewpoint by the modified replicator equation with non-uniform interaction rates in a simplified version of the prisoner's dilemma game (PDG). Copyright © 2012 Elsevier Ltd. All rights reserved.

Evolution of sparsity and modularity in a model of protein allostery

NASA Astrophysics Data System (ADS)

Hemery, Mathieu; Rivoire, Olivier

2015-04-01

The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary constraints may take is important to interpret the information in protein sequences. To study this problem, we introduce a simple but physical model of protein evolution where selection targets allostery, the functional coupling of distal sites on protein surfaces. This model shows how the geometrical organization of couplings between amino acids within a protein structure can depend crucially on its evolutionary history. In particular, two scenarios are found to generate a spatial concentration of functional constraints: high mutation rates and fluctuating selective pressures. This second scenario offers a plausible explanation for the high tolerance of natural proteins to mutations and for the spatial organization of their least tolerant amino acids, as revealed by sequence analysis and mutagenesis experiments. It also implies a faculty to adapt to new selective pressures that is consistent with observations. The model illustrates how several independent functional modules may emerge within the same protein structure, depending on the nature of past environmental fluctuations. Our model thus relates the evolutionary history of proteins to the geometry of their functional constraints, with implications for decoding and engineering protein sequences.

Thirst modulates a perception.

PubMed

Changizi, M A; Hall, W G

2001-01-01

Does thirst make you more likely to think you see water? Tales of thirsty desert travelers and oasis mirages are consistent with our intuitions that appetitive state can influence what we see in the world. Yet there has been surprisingly little scrutiny of this appetitive modulation of perception. We tested whether dehydrated subjects would be biased towards perceptions of transparency, a common property of water. We found that thirsty subjects have a greater tendency to perceive transparency in ambiguous stimuli, revealing an ecologically appropriate modulation of the visual system by a basic appetitive motive.

A comparative test of adaptive hypotheses for sexual size dimorphism in lizards.

PubMed

Cox, Robert M; Skelly, Stephanie L; John-Alder, Henry B

2003-07-01

It is commonly argued that sexual size dimorphism (SSD) in lizards has evolved in response to two primary, nonexclusive processes: (1) sexual selection for large male size, which confers an advantage in intrasexual mate competition (intrasexual selection hypothesis), and (2) natural selection for large female size, which confers a fecundity advantage (fecundity advantage hypothesis). However, outside of several well-studied lizard genera, the empirical support for these hypotheses has not been examined with appropriate phylogenetic control. We conducted a comparative phylogenetic analysis to test these hypotheses using literature data from 497 lizard populations representing 302 species and 18 families. As predicted by the intrasexual selection hypothesis, male aggression and territoriality are correlated with SSD, but evolutionary shifts in these categorical variables each explain less than 2% of the inferred evolutionary change in SSD. We found stronger correlations between SSD and continuous estimates of intrasexual selection such as male to female home range ratio and female home range size. These results are consistent with the criticism that categorical variables may obscure much of the actual variation in intrasexual selection intensity needed to explain patterns in SSD. In accordance with the fecundity advantage hypothesis, SSD is correlated with clutch size, reproductive frequency, and reproductive mode (but not fecundity slope, reduced major axis estimator of fecundity slope, length of reproductive season, or latitude). However, evolutionary shifts in clutch size explain less than 8% of the associated change in SSD, which also varies significantly in the absence of evolutionary shifts in reproductive frequency and mode. A multiple regression model retained territoriality and clutch size as significant predictors of SSD, but only 16% of the variation in SSD is explained using these variables. Intrasexual selection for large male size and fecundity selection for large female size have undoubtedly helped to shape patterns of SSD across lizards, but the comparative data at present provide only weak support for these hypotheses as general explanations for SSD in this group. Future work would benefit from the consideration of alternatives to these traditional evolutionary hypotheses, and the elucidation of proximate mechanisms influencing growth and SSD within populations.

Quantitative genetic correlation between trait and preference supports a sexually selected sperm process

PubMed Central

Simmons, Leigh W.; Kotiaho, Janne S.

2007-01-01

Sperm show patterns of rapid and divergent evolution that are characteristic of sexual selection. Sperm competition has been proposed as an important selective agent in the evolution of sperm morphology. However, several comparative analyses have revealed evolutionary associations between sperm length and female reproductive tract morphology that suggest patterns of male–female coevolution. In the dung beetle Onthophagus taurus, males with short sperm have a fertilization advantage that depends on the size of the female's sperm storage organ, the spermatheca; large spermathecae select for short sperm. Sperm length is heritable and is genetically correlated with male condition. Here we report significant additive genetic variation and heritability for spermatheca size and genetic covariance between spermatheca size and sperm length predicted by both the “good-sperm” and “sexy-sperm” models of postcopulatory female preference. Our data thus provide quantitative genetic support for the role of a sexually selected sperm process in the evolutionary divergence of sperm morphology, in much the same manner as precopulatory female preferences drive the evolutionary divergence of male secondary sexual traits. PMID:17921254

Fixation probabilities on superstars, revisited and revised.

PubMed

Jamieson-Lane, Alastair; Hauert, Christoph

2015-10-07

Population structures can be crucial determinants of evolutionary processes. For the Moran process on graphs certain structures suppress selective pressure, while others amplify it (Lieberman et al., 2005). Evolutionary amplifiers suppress random drift and enhance selection. Recently, some results for the most powerful known evolutionary amplifier, the superstar, have been invalidated by a counter example (Díaz et al., 2013). Here we correct the original proof and derive improved upper and lower bounds, which indicate that the fixation probability remains close to 1-1/(r(4)H) for population size N→∞ and structural parameter H⪢1. This correction resolves the differences between the two aforementioned papers. We also confirm that in the limit N,H→∞ superstars remain capable of eliminating random drift and hence of providing arbitrarily strong selective advantages to any beneficial mutation. In addition, we investigate the robustness of amplification in superstars and find that it appears to be a fragile phenomenon with respect to changes in the selection or mutation processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Promotion of cooperation in evolutionary game dynamics with local information.

PubMed

Liu, Xuesong; Pan, Qiuhui; He, Mingfeng

2018-01-21

In this paper, we propose a strategy-updating rule driven by local information, which is called Local process. Unlike the standard Moran process, the Local process does not require global information about the strategic environment. By analyzing the dynamical behavior of the system, we explore how the local information influences the fixation of cooperation in two-player evolutionary games. Under weak selection, the decreasing local information leads to an increase of the fixation probability when natural selection does not favor cooperation replacing defection. In the limit of sufficiently large selection, the analytical results indicate that the fixation probability increases with the decrease of the local information, irrespective of the evolutionary games. Furthermore, for the dominance of defection games under weak selection and for coexistence games, the decreasing of local information will lead to a speedup of a single cooperator taking over the population. Overall, to some extent, the local information is conducive to promoting the cooperation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Adaptations to sexual selection and sexual conflict: insights from experimental evolution and artificial selection.

PubMed

Edward, Dominic A; Fricke, Claudia; Chapman, Tracey

2010-08-27

Artificial selection and experimental evolution document natural selection under controlled conditions. Collectively, these techniques are continuing to provide fresh and important insights into the genetic basis of evolutionary change, and are now being employed to investigate mating behaviour. Here, we focus on how selection techniques can reveal the genetic basis of post-mating adaptations to sexual selection and sexual conflict. Alteration of the operational sex ratio of adult Drosophila over just a few tens of generations can lead to altered ejaculate allocation patterns and the evolution of resistance in females to the costly effects of elevated mating rates. We provide new data to show how male responses to the presence of rivals can evolve. For several traits, the way in which males responded to rivals was opposite in lines selected for male-biased, as opposed to female-biased, adult sex ratio. This shows that the manipulation of the relative intensity of intra- and inter-sexual selection can lead to replicable and repeatable effects on mating systems, and reveals the potential for significant contemporary evolutionary change. Such studies, with important safeguards, have potential utility for understanding sexual selection and sexual conflict across many taxa. We discuss how artificial selection studies combined with genomics will continue to deepen our knowledge of the evolutionary principles first laid down by Darwin 150 years ago.

Neuronal boost to evolutionary dynamics.

PubMed

de Vladar, Harold P; Szathmáry, Eörs

2015-12-06

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

Evolutionary engineering for industrial microbiology.

PubMed

Vanee, Niti; Fisher, Adam B; Fong, Stephen S

2012-01-01

Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

The one-third law of evolutionary dynamics.

PubMed

Ohtsuki, Hisashi; Bordalo, Pedro; Nowak, Martin A

2007-11-21

Evolutionary game dynamics in finite populations provide a new framework for studying selection of traits with frequency-dependent fitness. Recently, a "one-third law" of evolutionary dynamics has been described, which states that strategy A fixates in a B-population with selective advantage if the fitness of A is greater than that of B when A has a frequency 13. This relationship holds for all evolutionary processes examined so far, from the Moran process to games on graphs. However, the origin of the "number"13 is not understood. In this paper we provide an intuitive explanation by studying the underlying stochastic processes. We find that in one invasion attempt, an individual interacts on average with B-players twice as often as with A-players, which yields the one-third law. We also show that the one-third law implies that the average Malthusian fitness of A is positive.

Sexual Selection Halts the Relaxation of Protamine 2 among Rodents

PubMed Central

Lüke, Lena; Vicens, Alberto; Serra, Francois; Luque-Larena, Juan Jose; Dopazo, Hernán; Roldan, Eduardo R. S.; Gomendio, Montserrat

2011-01-01

Sexual selection has been proposed as the driving force promoting the rapid evolutionary changes observed in some reproductive genes including protamines. We test this hypothesis in a group of rodents which show marked differences in the intensity of sexual selection. Levels of sperm competition were not associated with the evolutionary rates of protamine 1 but, contrary to expectations, were negatively related to the evolutionary rate of cleaved- and mature-protamine 2. Since both domains were found to be under relaxation, our findings reveal an unforeseen role of sexual selection: to halt the degree of degeneration that proteins within families may experience due to functional redundancy. The degree of relaxation of protamine 2 in this group of rodents is such that in some species it has become dysfunctional and it is not expressed in mature spermatozoa. In contrast, protamine 1 is functionally conserved but shows directed positive selection on specific sites which are functionally relevant such as DNA-anchoring domains and phosphorylation sites. We conclude that in rodents protamine 2 is under relaxation and that sexual selection removes deleterious mutations among species with high levels of sperm competition to maintain the protein functional and the spermatozoa competitive. PMID:22216223

Intense natural selection preceded the invasion of new adaptive zones during the radiation of New World leaf-nosed bats.

PubMed

Rossoni, Daniela M; Assis, Ana Paula A; Giannini, Norberto P; Marroig, Gabriel

2017-09-11

The family Phyllostomidae, which evolved in the New World during the last 30 million years, represents one of the largest and most morphologically diverse mammal families. Due to its uniquely diverse functional morphology, the phyllostomid skull is presumed to have evolved under strong directional selection; however, quantitative estimation of the strength of selection in this extraordinary lineage has not been reported. Here, we used comparative quantitative genetics approaches to elucidate the processes that drove cranial evolution in phyllostomids. We also quantified the strength of selection and explored its association with dietary transitions and specialization along the phyllostomid phylogeny. Our results suggest that natural selection was the evolutionary process responsible for cranial diversification in phyllostomid bats. Remarkably, the strongest selection in the phyllostomid phylogeny was associated with dietary specialization and the origination of novel feeding habits, suggesting that the adaptive diversification of phyllostomid bats was triggered by ecological opportunities. These findings are consistent with Simpson's quantum evolutionary model of transitions between adaptive zones. The multivariate analyses used in this study provides a powerful tool for understanding the role of evolutionary processes in shaping phenotypic diversity in any group on both micro- and macroevolutionary scales.

Avoiding Local Optima with Interactive Evolutionary Robotics

DTIC Science & Technology

2012-07-09

the top of a flight of stairs selects for climbing ; suspending the robot and the target object above the ground and creating rungs between the two will...REPORT Avoiding Local Optimawith Interactive Evolutionary Robotics 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The main bottleneck in evolutionary... robotics has traditionally been the time required to evolve robot controllers. However with the continued acceleration in computational resources, the

Ecology, sexual selection and speciation.

PubMed

Maan, Martine E; Seehausen, Ole

2011-06-01

The spectacular diversity in sexually selected traits among animal taxa has inspired the hypothesis that divergent sexual selection can drive speciation. Unfortunately, speciation biologists often consider sexual selection in isolation from natural selection, even though sexually selected traits evolve in an ecological context: both preferences and traits are often subject to natural selection. Conversely, while behavioural ecologists may address ecological effects on sexual communication, they rarely measure the consequences for population divergence. Herein, we review the empirical literature addressing the mechanisms by which natural selection and sexual selection can interact during speciation. We find that convincing evidence for any of these scenarios is thin. However, the available data strongly support various diversifying effects that emerge from interactions between sexual selection and environmental heterogeneity. We suggest that evaluating the evolutionary consequences of these effects requires a better integration of behavioural, ecological and evolutionary research. © 2011 Blackwell Publishing Ltd/CNRS.

Adaptive landscape and functional diversity of Neotropical cichlids: implications for the ecology and evolution of Cichlinae (Cichlidae; Cichliformes).

PubMed

Arbour, J H; López-Fernández, H

2014-11-01

Morphological, lineage and ecological diversity can vary substantially even among closely related lineages. Factors that influence morphological diversification, especially in functionally relevant traits, can help to explain the modern distribution of disparity across phylogenies and communities. Multivariate axes of feeding functional morphology from 75 species of Neotropical cichlid and a stepwise-AIC algorithm were used to estimate the adaptive landscape of functional morphospace in Cichlinae. Adaptive landscape complexity and convergence, as well as the functional diversity of Cichlinae, were compared with expectations under null evolutionary models. Neotropical cichlid feeding function varied primarily between traits associated with ram feeding vs. suction feeding/biting and secondarily with oral jaw muscle size and pharyngeal crushing capacity. The number of changes in selective regimes and the amount of convergence between lineages was higher than expected under a null model of evolution, but convergence was not higher than expected under a similarly complex adaptive landscape. Functional disparity was compatible with an adaptive landscape model, whereas the distribution of evolutionary change through morphospace corresponded with a process of evolution towards a single adaptive peak. The continentally distributed Neotropical cichlids have evolved relatively rapidly towards a number of adaptive peaks in functional trait space. Selection in Cichlinae functional morphospace is more complex than expected under null evolutionary models. The complexity of selective constraints in feeding morphology has likely been a significant contributor to the diversity of feeding ecology in this clade. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Why are some people left-handed? An evolutionary perspective

PubMed Central

Llaurens, V.; Raymond, M.; Faurie, C.

2008-01-01

Since prehistoric times, left-handed individuals have been ubiquitous in human populations, exhibiting geographical frequency variations. Evolutionary explanations have been proposed for the persistence of the handedness polymorphism. Left-handedness could be favoured by negative frequency-dependent selection. Data have suggested that left-handedness, as the rare hand preference, could represent an important strategic advantage in fighting interactions. However, the fact that left-handedness occurs at a low frequency indicates that some evolutionary costs could be associated with left-handedness. Overall, the evolutionary dynamics of this polymorphism are not fully understood. Here, we review the abundant literature available regarding the possible mechanisms and consequences of left-handedness. We point out that hand preference is heritable, and report how hand preference is influenced by genetic, hormonal, developmental and cultural factors. We review the available information on potential fitness costs and benefits acting as selective forces on the proportion of left-handers. Thus, evolutionary perspectives on the persistence of this polymorphism in humans are gathered for the first time, highlighting the necessity for an assessment of fitness differences between right- and left-handers. PMID:19064347

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.

PubMed

Studer, Romain A; Penel, Simon; Duret, Laurent; Robinson-Rechavi, Marc

2008-09-01

A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.

Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards.

PubMed

Hagey, Travis J; Uyeda, Josef C; Crandell, Kristen E; Cheney, Jorn A; Autumn, Kellar; Harmon, Luke J

2017-10-01

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here, we ask whether convergent evolution of pad-bearing lizards has followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Evolutionary rescue in vertebrates: evidence, applications and uncertainty

PubMed Central

Vander Wal, E.; Garant, D.; Festa-Bianchet, M.; Pelletier, F.

2013-01-01

The current rapid rate of human-driven environmental change presents wild populations with novel conditions and stresses. Theory and experimental evidence for evolutionary rescue present a promising case for species facing environmental change persisting via adaptation. Here, we assess the potential for evolutionary rescue in wild vertebrates. Available information on evolutionary rescue was rare and restricted to abundant and highly fecund species that faced severe intentional anthropogenic selective pressures. However, examples from adaptive tracking in common species and genetic rescues in species of conservation concern provide convincing evidence in favour of the mechanisms of evolutionary rescue. We conclude that low population size, long generation times and limited genetic variability will result in evolutionary rescue occurring rarely for endangered species without intervention. Owing to the risks presented by current environmental change and the possibility of evolutionary rescue in nature, we suggest means to study evolutionary rescue by mapping genotype → phenotype → demography → fitness relationships, and priorities for applying evolutionary rescue to wild populations. PMID:23209171

Strategy selection in structured populations.

PubMed

Tarnita, Corina E; Ohtsuki, Hisashi; Antal, Tibor; Fu, Feng; Nowak, Martin A

2009-08-07

Evolutionary game theory studies frequency dependent selection. The fitness of a strategy is not constant, but depends on the relative frequencies of strategies in the population. This type of evolutionary dynamics occurs in many settings of ecology, infectious disease dynamics, animal behavior and social interactions of humans. Traditionally evolutionary game dynamics are studied in well-mixed populations, where the interaction between any two individuals is equally likely. There have also been several approaches to study evolutionary games in structured populations. In this paper we present a simple result that holds for a large variety of population structures. We consider the game between two strategies, A and B, described by the payoff matrix(abcd). We study a mutation and selection process. For weak selection strategy A is favored over B if and only if sigma a+b>c+sigma d. This means the effect of population structure on strategy selection can be described by a single parameter, sigma. We present the values of sigma for various examples including the well-mixed population, games on graphs, games in phenotype space and games on sets. We give a proof for the existence of such a sigma, which holds for all population structures and update rules that have certain (natural) properties. We assume weak selection, but allow any mutation rate. We discuss the relationship between sigma and the critical benefit to cost ratio for the evolution of cooperation. The single parameter, sigma, allows us to quantify the ability of a population structure to promote the evolution of cooperation or to choose efficient equilibria in coordination games.

Evolutionary dynamics on any population structure

NASA Astrophysics Data System (ADS)

Allen, Benjamin; Lippner, Gabor; Chen, Yu-Ting; Fotouhi, Babak; Momeni, Naghmeh; Yau, Shing-Tung; Nowak, Martin A.

2017-03-01

Evolution occurs in populations of reproducing individuals. The structure of a population can affect which traits evolve. Understanding evolutionary game dynamics in structured populations remains difficult. Mathematical results are known for special structures in which all individuals have the same number of neighbours. The general case, in which the number of neighbours can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class that suggests there is no efficient algorithm. Whether a simple solution for weak selection exists has remained unanswered. Here we provide a solution for weak selection that applies to any graph or network. Our method relies on calculating the coalescence times of random walks. We evaluate large numbers of diverse population structures for their propensity to favour cooperation. We study how small changes in population structure—graph surgery—affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.

Climate variability slows evolutionary responses of Colias butterflies to recent climate change.

PubMed

Kingsolver, Joel G; Buckley, Lauren B

2015-03-07

How does recent climate warming and climate variability alter fitness, phenotypic selection and evolution in natural populations? We combine biophysical, demographic and evolutionary models with recent climate data to address this question for the subalpine and alpine butterfly, Colias meadii, in the southern Rocky Mountains. We focus on predicting patterns of selection and evolution for a key thermoregulatory trait, melanin (solar absorptivity) on the posterior ventral hindwings, which affects patterns of body temperature, flight activity, adult and egg survival, and reproductive success in Colias. Both mean annual summer temperatures and thermal variability within summers have increased during the past 60 years at subalpine and alpine sites. At the subalpine site, predicted directional selection on wing absorptivity has shifted from generally positive (favouring increased wing melanin) to generally negative during the past 60 years, but there is substantial variation among years in the predicted magnitude and direction of selection and the optimal absorptivity. The predicted magnitude of directional selection at the alpine site declined during the past 60 years and varies substantially among years, but selection has generally been positive at this site. Predicted evolutionary responses to mean climate warming at the subalpine site since 1980 is small, because of the variability in selection and asymmetry of the fitness function. At both sites, the predicted effects of adaptive evolution on mean population fitness are much smaller than the fluctuations in mean fitness due to climate variability among years. Our analyses suggest that variation in climate within and among years may strongly limit evolutionary responses of ectotherms to mean climate warming in these habitats. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Communicative genes in the evolution of empathy and altruism.

PubMed

Buck, Ross

2011-11-01

This paper discusses spontaneous communication and its implications for understanding empathy and altruism. The question of the possibility of "true" altruism-giving up one's genetic potential in favor of the genetic potential of another-is a fundamental issue common to the biological, behavioral, and social sciences. Darwin regarded "social instincts and sympathies" to be critical to the social order, but the possibility of biologically-based prosocial motives and emotions was questioned when selection was interpreted as operating at the level of the gene. In the selfish gene hypothesis, Dawkins argued that the unit of evolutionary selection must be an active, germ-line replicator: a unit whose activities determine whether copies of it are made across evolutionary timescales. He argued that the only active replicator existing across evolutionary timescales is the gene, so that the "selfish gene" is a replicator motivated only to make copies of itself. The communicative gene hypothesis notes that genes function by communicating, and the phenotype communication involves not only the individual sending and receiving abilities of the individual genes involved, but also the relationship between them relative to other genes. Therefore the selection of communication as phenotype involves the selection of individual genes and also their relationship. Relationships become replicators, and are selected across evolutionary timescales including social relationships (e.g., sex, nurturance, dominance-submission). An interesting implication of this view: apparent altruism has been interpreted by selfish gene theorists as due to kin selection and reciprocity, in which the survival of kin and comrade indirectly favor the genetic potential of the altruist. From the viewpoint of the communicative gene hypothesis, rather than underlying altruism, kin selection and reciprocity are ways of restricting altruism to kin and comrade: they are mechanisms not of altruism but of xenophobia.

Assessing Multivariate Constraints to Evolution across Ten Long-Term Avian Studies

PubMed Central

Teplitsky, Celine; Tarka, Maja; Møller, Anders P.; Nakagawa, Shinichi; Balbontín, Javier; Burke, Terry A.; Doutrelant, Claire; Gregoire, Arnaud; Hansson, Bengt; Hasselquist, Dennis; Gustafsson, Lars; de Lope, Florentino; Marzal, Alfonso; Mills, James A.; Wheelwright, Nathaniel T.; Yarrall, John W.; Charmantier, Anne

2014-01-01

Background In a rapidly changing world, it is of fundamental importance to understand processes constraining or facilitating adaptation through microevolution. As different traits of an organism covary, genetic correlations are expected to affect evolutionary trajectories. However, only limited empirical data are available. Methodology/Principal Findings We investigate the extent to which multivariate constraints affect the rate of adaptation, focusing on four morphological traits often shown to harbour large amounts of genetic variance and considered to be subject to limited evolutionary constraints. Our data set includes unique long-term data for seven bird species and a total of 10 populations. We estimate population-specific matrices of genetic correlations and multivariate selection coefficients to predict evolutionary responses to selection. Using Bayesian methods that facilitate the propagation of errors in estimates, we compare (1) the rate of adaptation based on predicted response to selection when including genetic correlations with predictions from models where these genetic correlations were set to zero and (2) the multivariate evolvability in the direction of current selection to the average evolvability in random directions of the phenotypic space. We show that genetic correlations on average decrease the predicted rate of adaptation by 28%. Multivariate evolvability in the direction of current selection was systematically lower than average evolvability in random directions of space. These significant reductions in the rate of adaptation and reduced evolvability were due to a general nonalignment of selection and genetic variance, notably orthogonality of directional selection with the size axis along which most (60%) of the genetic variance is found. Conclusions These results suggest that genetic correlations can impose significant constraints on the evolution of avian morphology in wild populations. This could have important impacts on evolutionary dynamics and hence population persistence in the face of rapid environmental change. PMID:24608111

Sexual and natural selection in the evolution of extended phenotypes: the use of green nesting material in starlings.

PubMed

Rubalcaba, J G; Polo, V; Maia, R; Rubenstein, D R; Veiga, J P

2016-08-01

Although sexual selection is typically considered the predominant force driving the evolution of ritualized sexual behaviours, natural selection may also play an important and often underappreciated role. The use of green aromatic plants among nesting birds has been interpreted as a component of extended phenotype that evolved either via natural selection due to potential sanitary functions or via sexual selection as a signal of male attractiveness. Here, we compared both hypotheses using comparative methods in starlings, a group where this behaviour is widespread. We found that the use of green plants was positively related to male-biased size dimorphism and that it was most likely to occur among cavity-nesting species. These results suggest that this behaviour is likely favoured by sexual selection, but also related to its sanitary use in response to higher parasite loads in cavities. We speculate that the use of green plants in starlings may be facilitated by cavity nesting and was subsequently co-opted as a sexual signal by males. Our results represent an example of how an extended phenotypic component of males becomes sexually selected by females. Thus, both natural selection and sexual selection are necessary to fully understand the evolution of ritualized behaviours involved in courtship. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes

PubMed Central

2011-01-01

Background Changes in transcriptional orientation (“CTOs”) occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication and transcription and an increase in mutation rate. However, CTOs do not always lead to the replication-transcription confrontation. Furthermore, CTOs may cause deleterious disruptions of operon structure and/or gene regulations. The currently existing CTOs may indicate relaxation of selection pressure. Therefore, it is of interest to investigate whether CTOs have an independent effect on the evolutionary rates of the affected genes, and whether these genes are subject to any type of selection pressure in prokaryotes. Methods Three closely related enterbacteria, Escherichia coli, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium, were selected for comparisons of synonymous (dS) and nonsynonymous (dN) substitution rate between the genes that have experienced changes in transcriptional orientation (changed-orientation genes, “COGs”) and those that do not (same-orientation genes, “SOGs”). The dN/dS ratio was also derived to evaluate the selection pressure on the analyzed genes. Confounding factors in the estimation of evolutionary rates, such as gene essentiality, gene expression level, replication-transcription confrontation, and decreased dS at gene terminals were controlled in the COG-SOG comparisons. Results We demonstrate that COGs have significantly higher dN and dS than SOGs when a series of confounding factors are controlled. However, the dN/dS ratios are similar between the two gene groups, suggesting that the increase in dS can sufficiently explain the increase in dN in COGs. Therefore, the increases in evolutionary rates in COGs may be mainly mutation-driven. Conclusions Here we show that CTOs can increase the evolutionary rates of the affected genes. This effect is independent of the replication-transcription confrontation, which is suggested to be the major cause of inversion-associated evolutionary rate increases. The real cause of such evolutionary rate increases remains unclear but is worth further explorations. PMID:22152004

An invasive plant alters phenotypic selection on the vegetative growth of a native congener.

PubMed

Beans, Carolyn M; Roach, Deborah A

2015-02-01

The ecological consequences of plant competition have frequently been tested, but the evolutionary outcomes of these interactions have gone largely unexplored. The study of species invasions can make an important contribution to this field of research by allowing us to watch ecological and evolutionary processes unfold as a novel species is integrated into a plant community. We explored the ecological and evolutionary impact of an invasive jewelweed, Impatiens glandulifera, on a closely related native congener, I. capensis and asked: (1) Does the presence of the invasive jewelweed alter the fitness of native jewelweed populations? (2) Does the invasive jewelweed affect the vegetative growth of the native congener? and (3) Does the invasive jewelweed alter phenotypic selection on the vegetative traits of the native congener? We used a greenhouse competition experiment, an invasive species removal field experiment, and a survey of natural populations. We show that when the invasive jewelweed is present, phenotypic selection favors native jewelweed individuals investing less in rapid upward growth and more in branching and fruiting potential through the production of nodes. This research demonstrates that invasive plants have the potential to greatly alter natural selection on native competitors. Studies investigating altered selection in invaded communities can reveal the potential evolutionary impact of invasive competitors, while deepening our understanding of the more general role of competition in driving plant evolution and permitting species coexistence. © 2015 Botanical Society of America, Inc.

The great opportunity: Evolutionary applications to medicine and public health.

PubMed

Nesse, Randolph M; Stearns, Stephen C

2008-02-01

Evolutionary biology is an essential basic science for medicine, but few doctors and medical researchers are familiar with its most relevant principles. Most medical schools have geneticists who understand evolution, but few have even one evolutionary biologist to suggest other possible applications. The canyon between evolutionary biology and medicine is wide. The question is whether they offer each other enough to make bridge building worthwhile. What benefits could be expected if evolution were brought fully to bear on the problems of medicine? How would studying medical problems advance evolutionary research? Do doctors need to learn evolution, or is it valuable mainly for researchers? What practical steps will promote the application of evolutionary biology in the areas of medicine where it offers the most? To address these questions, we review current and potential applications of evolutionary biology to medicine and public health. Some evolutionary technologies, such as population genetics, serial transfer production of live vaccines, and phylogenetic analysis, have been widely applied. Other areas, such as infectious disease and aging research, illustrate the dramatic recent progress made possible by evolutionary insights. In still other areas, such as epidemiology, psychiatry, and understanding the regulation of bodily defenses, applying evolutionary principles remains an open opportunity. In addition to the utility of specific applications, an evolutionary perspective fundamentally challenges the prevalent but fundamentally incorrect metaphor of the body as a machine designed by an engineer. Bodies are vulnerable to disease - and remarkably resilient - precisely because they are not machines built from a plan. They are, instead, bundles of compromises shaped by natural selection in small increments to maximize reproduction, not health. Understanding the body as a product of natural selection, not design, offers new research questions and a framework for making medical education more coherent. We conclude with recommendations for actions that would better connect evolutionary biology and medicine in ways that will benefit public health. It is our hope that faculty and students will send this article to their undergraduate and medical school Deans, and that this will initiate discussions about the gap, the great opportunity, and action plans to bring the full power of evolutionary biology to bear on human health problems.

Demographic drivers of age-dependent sexual selection.

PubMed

Martin, A M; Festa-Bianchet, M; Coltman, D W; Pelletier, F

2016-07-01

Sexual selection has a critical role in evolution, and it is fundamental to identify what ecological factors drive its variation. Disentangling the ecological correlates of sexual selection over the long term, however, is challenging and has rarely been done in nature. We sought to assess how demographic changes influenced the intensity, direction and form of sexual selection and whether selective pressures varied with age. We tested whether breeder sex ratio, number of competitors and age structure influenced selection differentials on horn length of wild bighorn rams (Ovis canadensis) of different age classes on Ram Mountain, Alberta. We used 21 years of data including a detailed pedigree, demographic parameters and repeated morphological measurements. Sexual selection on horn length of males of all ages was directional and positive. Selection intensity increased with the number of competitors, reflecting male-male encounter rate during the rut, but was independent of breeder sex ratio or age structure. This result can also be linked to changes in population size because the number of competitors was highly correlated to total number of sheep. This demographic effect likely arises from age-dependent mating tactics. Males aged 2-4 years are weakly competitive and experienced stronger sexual selection as they accounted for a greater proportion of all males. Selection experienced by mature males appeared independent of demography. Our study provides a rare description of the demographic determinants of sexual selection in nature. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks

PubMed Central

2011-01-01

Background Protein domains are globular structures of independently folded polypeptides that exert catalytic or binding activities. Their sequences are recognized as evolutionary units that, through genome recombination, constitute protein repertoires of linkage patterns. Via mutations, domains acquire modified functions that contribute to the fitness of cells and organisms. Recent studies have addressed the evolutionary selection that may have shaped the functions of individual domains and the emergence of particular domain combinations, which led to new cellular functions in multi-cellular animals. This study focuses on modeling domain linkage globally and investigates evolutionary implications that may be revealed by novel computational analysis. Results A survey of 77 completely sequenced eukaryotic genomes implies a potential hierarchical and modular organization of biological functions in most living organisms. Domains in a genome or multiple genomes are modeled as a network of hetero-duplex covalent linkages, termed bigrams. A novel computational technique is introduced to decompose such networks, whereby the notion of domain "networking versatility" is derived and measured. The most and least "versatile" domains (termed "core domains" and "peripheral domains" respectively) are examined both computationally via sequence conservation measures and experimentally using selected domains. Our study suggests that such a versatility measure extracted from the bigram networks correlates with the adaptivity of domains during evolution, where the network core domains are highly adaptive, significantly contrasting the network peripheral domains. Conclusions Domain recombination has played a major part in the evolution of eukaryotes attributing to genome complexity. From a system point of view, as the results of selection and constant refinement, networks of domain linkage are structured in a hierarchical modular fashion. Domains with high degree of networking versatility appear to be evolutionary adaptive, potentially through functional innovations. Domain bigram networks are informative as a model of biological functions. The networking versatility indices extracted from such networks for individual domains reflect the strength of evolutionary selection that the domains have experienced. PMID:21849086

Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks.

PubMed

Xie, Xueying; Jin, Jing; Mao, Yongyi

2011-08-18

Protein domains are globular structures of independently folded polypeptides that exert catalytic or binding activities. Their sequences are recognized as evolutionary units that, through genome recombination, constitute protein repertoires of linkage patterns. Via mutations, domains acquire modified functions that contribute to the fitness of cells and organisms. Recent studies have addressed the evolutionary selection that may have shaped the functions of individual domains and the emergence of particular domain combinations, which led to new cellular functions in multi-cellular animals. This study focuses on modeling domain linkage globally and investigates evolutionary implications that may be revealed by novel computational analysis. A survey of 77 completely sequenced eukaryotic genomes implies a potential hierarchical and modular organization of biological functions in most living organisms. Domains in a genome or multiple genomes are modeled as a network of hetero-duplex covalent linkages, termed bigrams. A novel computational technique is introduced to decompose such networks, whereby the notion of domain "networking versatility" is derived and measured. The most and least "versatile" domains (termed "core domains" and "peripheral domains" respectively) are examined both computationally via sequence conservation measures and experimentally using selected domains. Our study suggests that such a versatility measure extracted from the bigram networks correlates with the adaptivity of domains during evolution, where the network core domains are highly adaptive, significantly contrasting the network peripheral domains. Domain recombination has played a major part in the evolution of eukaryotes attributing to genome complexity. From a system point of view, as the results of selection and constant refinement, networks of domain linkage are structured in a hierarchical modular fashion. Domains with high degree of networking versatility appear to be evolutionary adaptive, potentially through functional innovations. Domain bigram networks are informative as a model of biological functions. The networking versatility indices extracted from such networks for individual domains reflect the strength of evolutionary selection that the domains have experienced.

Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies.

PubMed

Mina, Marco; Raynaud, Franck; Tavernari, Daniele; Battistello, Elena; Sungalee, Stephanie; Saghafinia, Sadegh; Laessle, Titouan; Sanchez-Vega, Francisco; Schultz, Nikolaus; Oricchio, Elisa; Ciriello, Giovanni

2017-08-14

Cancer evolves through the emergence and selection of molecular alterations. Cancer genome profiling has revealed that specific events are more or less likely to be co-selected, suggesting that the selection of one event depends on the others. However, the nature of these evolutionary dependencies and their impact remain unclear. Here, we designed SELECT, an algorithmic approach to systematically identify evolutionary dependencies from alteration patterns. By analyzing 6,456 genomes from multiple tumor types, we constructed a map of oncogenic dependencies associated with cellular pathways, transcriptional readouts, and therapeutic response. Finally, modeling of cancer evolution shows that alteration dependencies emerge only under conditional selection. These results provide a framework for the design of strategies to predict cancer progression and therapeutic response. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

PubMed Central

Huang, Lei; Liao, Li; Wu, Cathy H.

2016-01-01

Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

Evolutionary perspectives on learning: conceptual and methodological issues in the study of adaptive specializations.

PubMed

Krause, Mark A

2015-07-01

Inquiry into evolutionary adaptations has flourished since the modern synthesis of evolutionary biology. Comparative methods, genetic techniques, and various experimental and modeling approaches are used to test adaptive hypotheses. In psychology, the concept of adaptation is broadly applied and is central to comparative psychology and cognition. The concept of an adaptive specialization of learning is a proposed account for exceptions to general learning processes, as seen in studies of Pavlovian conditioning of taste aversions, sexual responses, and fear. The evidence generally consists of selective associations forming between biologically relevant conditioned and unconditioned stimuli, with conditioned responses differing in magnitude, persistence, or other measures relative to non-biologically relevant stimuli. Selective associations for biologically relevant stimuli may suggest adaptive specializations of learning, but do not necessarily confirm adaptive hypotheses as conceived of in evolutionary biology. Exceptions to general learning processes do not necessarily default to an adaptive specialization explanation, even if experimental results "make biological sense". This paper examines the degree to which hypotheses of adaptive specializations of learning in sexual and fear response systems have been tested using methodologies developed in evolutionary biology (e.g., comparative methods, quantitative and molecular genetics, survival experiments). A broader aim is to offer perspectives from evolutionary biology for testing adaptive hypotheses in psychological science.

Darwinian demons, evolutionary complexity, and information maximization.

PubMed

Krakauer, David C

2011-09-01

Natural selection is shown to be an extended instance of a Maxwell's demon device. A demonic selection principle is introduced that states that organisms cannot exceed the complexity of their selective environment. Thermodynamic constraints on error repair impose a fundamental limit to the rate that information can be transferred from the environment (via the selective demon) to the genome. Evolved mechanisms of learning and inference can overcome this limitation, but remain subject to the same fundamental constraint, such that plastic behaviors cannot exceed the complexity of reward signals. A natural measure of evolutionary complexity is provided by mutual information, and niche construction activity--the organismal contribution to the construction of selection pressures--might in principle lead to its increase, bounded by thermodynamic free energy required for error correction.

Out-of-transit Refracted Light in the Atmospheres of Transiting and Non-transiting Exoplanets

NASA Astrophysics Data System (ADS)

Dalba, Paul A.

2017-10-01

Before an exoplanet transit, atmospheric refraction bends light into the line of sight of an observer. The refracted light forms a stellar mirage—a distorted secondary image of the host star. I model this phenomenon and the resultant out-of-transit flux increase across a comprehensive exoplanetary parameter space. At visible wavelengths, Rayleigh scattering limits the detectability of stellar mirages in most exoplanetary systems with semimajor axes ≲ 6 {au}. A notable exception is almost any planet orbiting a late M or ultra-cool dwarf star at ≳ 0.5 {au}, where the maximum relative flux increase is >50 parts per million. Based partly on previous work, I propose that the importance of refraction in an exoplanet system is governed by two angles: the orbital distance divided by the stellar radius and the total deflection achieved by a ray in the optically thin portion of the atmosphere. Atmospheric lensing events caused by non-transiting exoplanets, which allow for exoplanet detection and atmospheric characterization, are also investigated. I derive the basic formalism to determine the total signal-to-noise ratio of an atmospheric lensing event, with application to Kepler data. It is unlikely that out-of-transit refracted light signals are clearly present in Kepler data due to Rayleigh scattering and the bias toward short-period exoplanets. However, observations at long wavelengths (e.g., the near-infrared) are significantly more likely to detect stellar mirages. Lastly, I discuss the potential for the Transiting Exoplanet Survey Satellite to detect refracted light and consider novel science cases enabled by refracted light spectra from the James Webb Space Telescope.

Change and aging senescence as an adaptation.

PubMed

Martins, André C R

2011-01-01

Understanding why we age is a long-lived open problem in evolutionary biology. Aging is prejudicial to the individual, and evolutionary forces should prevent it, but many species show signs of senescence as individuals age. Here, I will propose a model for aging based on assumptions that are compatible with evolutionary theory: i) competition is between individuals; ii) there is some degree of locality, so quite often competition will be between parents and their progeny; iii) optimal conditions are not stationary, and mutation helps each species to keep competitive. When conditions change, a senescent species can drive immortal competitors to extinction. This counter-intuitive result arises from the pruning caused by the death of elder individuals. When there is change and mutation, each generation is slightly better adapted to the new conditions, but some older individuals survive by chance. Senescence can eliminate those from the genetic pool. Even though individual selection forces can sometimes win over group selection ones, it is not exactly the individual that is selected but its lineage. While senescence damages the individuals and has an evolutionary cost, it has a benefit of its own. It allows each lineage to adapt faster to changing conditions. We age because the world changes.

A real negative selection algorithm with evolutionary preference for anomaly detection

NASA Astrophysics Data System (ADS)

Yang, Tao; Chen, Wen; Li, Tao

2017-04-01

Traditional real negative selection algorithms (RNSAs) adopt the estimated coverage (c0) as the algorithm termination threshold, and generate detectors randomly. With increasing dimensions, the data samples could reside in the low-dimensional subspace, so that the traditional detectors cannot effectively distinguish these samples. Furthermore, in high-dimensional feature space, c0 cannot exactly reflect the detectors set coverage rate for the nonself space, and it could lead the algorithm to be terminated unexpectedly when the number of detectors is insufficient. These shortcomings make the traditional RNSAs to perform poorly in high-dimensional feature space. Based upon "evolutionary preference" theory in immunology, this paper presents a real negative selection algorithm with evolutionary preference (RNSAP). RNSAP utilizes the "unknown nonself space", "low-dimensional target subspace" and "known nonself feature" as the evolutionary preference to guide the generation of detectors, thus ensuring the detectors can cover the nonself space more effectively. Besides, RNSAP uses redundancy to replace c0 as the termination threshold, in this way RNSAP can generate adequate detectors under a proper convergence rate. The theoretical analysis and experimental result demonstrate that, compared to the classical RNSA (V-detector), RNSAP can achieve a higher detection rate, but with less detectors and computing cost.

HOW TO STUDY ADAPTATION (AND WHY TO DO IT THAT WAY).

PubMed

Olson, Mark E; Arroyo-Santos, Alfonso

2015-06-01

Some adaptationist explanations are regarded as maximally solid and others fanciful just-so stories. Just-so stories are explanations based on very little evidence. Lack of evidence leads to circular-sounding reasoning: "this trait was shaped by selection in unseen ancestral populations and this selection must have occurred because the trait is present." Well-supported adaptationist explanations include evidence that is not only abundant but selected from comparative, populational, and optimality perspectives, the three adaptationist subdisciplines. Each subdiscipline obtains its broad relevance in evolutionary biology via assumptions that can only be tested with the methods of the other subdisciplines. However, even in the best-supported explanations, assumptions regarding variation, heritability, and fitness in unseen ancestral populations are always present. These assumptions are accepted given how well they would explain the data if they were true. This means that some degree of "circularity" is present in all evolutionary explanations. Evolutionary explanation corresponds not to a deductive structure, as biologists usually assert, but instead to ones such as abduction or Bayesianism. With these structures in mind, we show the way to a healthier view of "circularity" in evolutionary biology and why integration across the comparative, populational, and optimality approaches is necessary.

Evolution of Swarming Behavior Is Shaped by How Predators Attack.

PubMed

Olson, Randal S; Knoester, David B; Adami, Christoph

2016-01-01

Animal grouping behaviors have been widely studied due to their implications for understanding social intelligence, collective cognition, and potential applications in engineering, artificial intelligence, and robotics. An important biological aspect of these studies is discerning which selection pressures favor the evolution of grouping behavior. In the past decade, researchers have begun using evolutionary computation to study the evolutionary effects of these selection pressures in predator-prey models. The selfish herd hypothesis states that concentrated groups arise because prey selfishly attempt to place their conspecifics between themselves and the predator, thus causing an endless cycle of movement toward the center of the group. Using an evolutionary model of a predator-prey system, we show that how predators attack is critical to the evolution of the selfish herd. Following this discovery, we show that density-dependent predation provides an abstraction of Hamilton's original formulation of domains of danger. Finally, we verify that density-dependent predation provides a sufficient selective advantage for prey to evolve the selfish herd in response to predation by coevolving predators. Thus, our work corroborates Hamilton's selfish herd hypothesis in a digital evolutionary model, refines the assumptions of the selfish herd hypothesis, and generalizes the domain of danger concept to density-dependent predation.

A Case-by-Case Evolutionary Analysis of Four Imprinted Retrogenes

PubMed Central

McCole, Ruth B; Loughran, Noeleen B; Chahal, Mandeep; Fernandes, Luis P; Roberts, Roland G; Fraternali, Franca; O'Connell, Mary J; Oakey, Rebecca J

2011-01-01

Retroposition is a widespread phenomenon resulting in the generation of new genes that are initially related to a parent gene via very high coding sequence similarity. We examine the evolutionary fate of four retrogenes generated by such an event; mouse Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1. These genes are all subject to the epigenetic phenomenon of parental imprinting. We first provide new data on the age of these retrogene insertions. Using codon-based models of sequence evolution, we show these retrogenes have diverse evolutionary trajectories, including divergence from the parent coding sequence under positive selection pressure, purifying selection pressure maintaining parent-retrogene similarity, and neutral evolution. Examination of the expression pattern of retrogenes shows an atypical, broad pattern across multiple tissues. Protein 3D structure modeling reveals that a positively selected residue in U2af1-rs1, not shared by its parent, may influence protein conformation. Our case-by-case analysis of the evolution of four imprinted retrogenes reveals that this interesting class of imprinted genes, while similar in regulation and sequence characteristics, follow very varied evolutionary paths. PMID:21166792

Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the 'ghost of selection past' and quantify the 'drift debt'.

PubMed

Gilroy, D L; Phillips, K P; Richardson, D S; van Oosterhout, C

2017-07-01

Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a postbottlenecked population is challenging due to the potentially overriding effects of drift. Toll-like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterized variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five of seven TLR loci were polymorphic, which is in sharp contrast to the low genomewide variation observed. However, standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR locus. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent-based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the prebottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the 'ghost of selection past'. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such 'drift debt' occurs when a gene pool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Inference of Evolutionary Forces Acting on Human Biological Pathways

PubMed Central

Daub, Josephine T.; Dupanloup, Isabelle; Robinson-Rechavi, Marc; Excoffier, Laurent

2015-01-01

Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints than other genes and that their evolutionary response is correlated. We then introduce a new procedure to detect selection at the pathway level based on a decomposition of the classical McDonald–Kreitman test extended to multiple genes. This new test, called 2DNS, detects outlier gene sets and takes into account past demographic effects and evolutionary constraints specific to gene sets. Selective forces acting on gene sets can be easily identified by a mere visual inspection of the position of the gene sets relative to their two-dimensional null distribution. We thus find several outlier gene sets that show signals of positive, balancing, or purifying selection but also others showing an ancient relaxation of selective constraints. The principle of the 2DNS test can also be applied to other genomic contrasts. For instance, the comparison of patterns of polymorphisms private to African and non-African populations reveals that most pathways show a higher proportion of nonsynonymous mutations in non-Africans than in Africans, potentially due to different demographic histories and selective pressures. PMID:25971280

Using geometric morphometric visualizations of directional selection gradients to investigate morphological differentiation.

PubMed

Weaver, Timothy D; Gunz, Philipp

2018-04-01

Researchers studying extant and extinct taxa are often interested in identifying the evolutionary processes that have lead to the morphological differences among the taxa. Ideally, one could distinguish the influences of neutral evolutionary processes (genetic drift, mutation) from natural selection, and in situations for which selection is implicated, identify the targets of selection. The directional selection gradient is an effective tool for investigating evolutionary process, because it can relate form (size and shape) differences between taxa to the variation and covariation found within taxa. However, although most modern morphometric analyses use the tools of geometric morphometrics (GM) to analyze landmark data, to date, selection gradients have mainly been calculated from linear measurements. To address this methodological gap, here we present a GM approach for visualizing and comparing between-taxon selection gradients with each other, associated difference vectors, and "selection" gradients from neutral simulations. To exemplify our approach, we use a dataset of 347 three-dimensional landmarks and semilandmarks recorded on the crania of 260 primate specimens (112 humans, 67 common chimpanzees, 36 bonobos, 45 gorillas). Results on this example dataset show how incorporating geometric information can provide important insights into the evolution of the human braincase, and serve to demonstrate the utility of our approach for understanding morphological evolution. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Expected utility violations evolve under status-based selection mechanisms.

PubMed

Dickson, Eric S

2008-10-07

The expected utility theory of decision making under uncertainty, a cornerstone of modern economics, assumes that humans linearly weight "utilities" for different possible outcomes by the probabilities with which these outcomes occur. Despite the theory's intuitive appeal, both from normative and from evolutionary perspectives, many experiments demonstrate systematic, though poorly understood, patterns of deviation from EU predictions. This paper offers a novel theoretical account of such patterns of deviation by demonstrating that EU violations can emerge from evolutionary selection when individual "status" affects inclusive fitness. In humans, battles for resources and social standing involve high-stakes decision making, and assortative mating ensures that status matters for fitness outcomes. The paper therefore proposes grounding the study of decision making under uncertainty in an evolutionary game-theoretic framework.

Aspiration dynamics of multi-player games in finite populations

PubMed Central

Du, Jinming; Wu, Bin; Altrock, Philipp M.; Wang, Long

2014-01-01

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics. PMID:24598208

Genetic basis and fitness correlates of dynamic carotenoid-based ornamental coloration in male and female common kestrels Falco tinnunculus.

PubMed

Vergara, P; Fargallo, J A; Martínez-Padilla, J

2015-01-01

Knowledge of the genetic basis of sexual ornaments is essential to understand their evolution through sexual selection. Although carotenoid-based ornaments have been instrumental in the study of sexual selection, given the inability of animals to synthesize carotenoids de novo, they are generally assumed to be influenced solely by environmental variation. However, very few studies have directly estimated the role of genes and the environment in shaping variation in carotenoid-based traits. Using long-term individual-based data, we here explore the evolutionary potential of a dynamic, carotenoid-based ornament (namely skin coloration), in male and female common kestrels. We first estimate the amount of genetic variation underlying variation in hue, chroma and brightness. After correcting for sex differences, the chroma of the orange-yellow eye ring coloration was significantly heritable (h2±SE=0.40±0.17), whereas neither hue (h2=0) nor brightness (h2=0.02) was heritable. Second, we estimate the strength and shape of selection acting upon chromatic (hue and chroma) and achromatic (brightness) variation and show positive and negative directional selection on female but not male chroma and hue, respectively, whereas brightness was unrelated to fitness in both sexes. This suggests that different components of carotenoid-based signals traits may show different evolutionary dynamics. Overall, we show that carotenoid-based coloration is a complex and multifaceted trait. If we are to gain a better understanding of the processes responsible for the generation and maintenance of variation in carotenoid-based coloration, these complexities need to be taken into account. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Aspiration dynamics of multi-player games in finite populations.

PubMed

Du, Jinming; Wu, Bin; Altrock, Philipp M; Wang, Long

2014-05-06

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics.

Geographic variation of life-history traits in the sand lizard, Lacerta agilis: testing Darwin's fecundity-advantage hypothesis.

PubMed

Roitberg, E S; Eplanova, G V; Kotenko, T I; Amat, F; Carretero, M A; Kuranova, V N; Bulakhova, N A; Zinenko, O I; Yakovlev, V A

2015-03-01

The fecundity-advantage hypothesis (FAH) explains larger female size relative to male size as a correlated response to fecundity selection. We explored FAH by investigating geographic variation in female reproductive output and its relation to sexual size dimorphism (SSD) in Lacerta agilis, an oviparous lizard occupying a major part of temperate Eurasia. We analysed how sex-specific body size and SSD are associated with two putative indicators of fecundity selection intensity (clutch size and the slope of the clutch size-female size relationship) and with two climatic variables throughout the species range and across two widespread evolutionary lineages. Variation within the lineages provides no support for FAH. In contrast, the divergence between the lineages is in line with FAH: the lineage with consistently female-biased SSD (L. a. agilis) exhibits higher clutch size and steeper fecundity slope than the lineage with an inconsistent and variable SSD (L. a. exigua). L. a. agilis shows lower offspring size (egg mass, hatchling mass) and higher clutch mass relative to female mass than L. a. exigua, that is both possible ways to enhance offspring number are exerted. As the SSD difference is due to male size (smaller males in L. a. agilis), fecundity selection favouring larger females, together with viability selection for smaller size in both sexes, would explain the female-biased SSD and reproductive characteristics of L. a. agilis. The pattern of intraspecific life-history divergence in L. agilis is strikingly similar to that between oviparous and viviparous populations of a related species Zootoca vivipara. Evolutionary implications of this parallelism are discussed. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Genetic drift and selection in many-allele range expansions.

PubMed

Weinstein, Bryan T; Lavrentovich, Maxim O; Möbius, Wolfram; Murray, Andrew W; Nelson, David R

2017-12-01

We experimentally and numerically investigate the evolutionary dynamics of four competing strains of E. coli with differing expansion velocities in radially expanding colonies. We compare experimental measurements of the average fraction, correlation functions between strains, and the relative rates of genetic domain wall annihilations and coalescences to simulations modeling the population as a one-dimensional ring of annihilating and coalescing random walkers with deterministic biases due to selection. The simulations reveal that the evolutionary dynamics can be collapsed onto master curves governed by three essential parameters: (1) an expansion length beyond which selection dominates over genetic drift; (2) a characteristic angular correlation describing the size of genetic domains; and (3) a dimensionless constant quantifying the interplay between a colony's curvature at the frontier and its selection length scale. We measure these parameters with a new technique that precisely measures small selective differences between spatially competing strains and show that our simulations accurately predict the dynamics without additional fitting. Our results suggest that the random walk model can act as a useful predictive tool for describing the evolutionary dynamics of range expansions composed of an arbitrary number of genotypes with different fitnesses.

Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks

PubMed Central

Fortunato, Angelo; Boddy, Amy; Mallo, Diego; Aktipis, Athena; Maley, Carlo C.; Pepper, John W.

2017-01-01

Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research. In this review, we discuss the differences and similarities between evolution among somatic cells versus evolution among organisms. We review what is known about the parameters and rate of evolution in neoplasms, as well as evidence for adaptation. We conclude that adaptation is a useful framework that accurately explains the defining characteristics of cancer. Further, convergent evolution through natural selection provides the only satisfying explanation both for how a group of diverse pathologies have enough in common to usefully share the descriptive label of “cancer” and for why this convergent condition becomes life-threatening. PMID:28148564

Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks.

PubMed

Fortunato, Angelo; Boddy, Amy; Mallo, Diego; Aktipis, Athena; Maley, Carlo C; Pepper, John W

2017-02-01

Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research. In this review, we discuss the differences and similarities between evolution among somatic cells versus evolution among organisms. We review what is known about the parameters and rate of evolution in neoplasms, as well as evidence for adaptation. We conclude that adaptation is a useful framework that accurately explains the defining characteristics of cancer. Further, convergent evolution through natural selection provides the only satisfying explanation both for how a group of diverse pathologies have enough in common to usefully share the descriptive label of "cancer" and for why this convergent condition becomes life-threatening. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Reconstructed ancestral enzymes reveal that negative selection drove the evolution of substrate specificity in ADP-dependent kinases.

PubMed

Castro-Fernandez, Víctor; Herrera-Morande, Alejandra; Zamora, Ricardo; Merino, Felipe; Gonzalez-Ordenes, Felipe; Padilla-Salinas, Felipe; Pereira, Humberto M; Brandão-Neto, Jose; Garratt, Richard C; Guixe, Victoria

2017-09-22

One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales , Methanosarcinales , and Methanococcales , as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes. To do so, we studied five key resurrected ancestral enzymes as well as their extant counterparts. We found that a major shift in function from a bifunctional ancestor that could phosphorylate either glucose or fructose 6-phosphate (fructose-6-P) as a substrate to a fructose 6-P-specific enzyme was started by a single amino acid substitution resulting in negative selection with a ground-state mode against glucose and a subsequent 1,600-fold change in specificity of the ancestral protein. This change rendered the residual phosphorylation of glucose a promiscuous and physiologically irrelevant activity, highlighting how promiscuity may be an evolutionary vestige of ancestral enzyme activities, which have been eliminated over time. We also could reconstruct the evolutionary history of substrate utilization by using an evolutionary model of discrete binary characters, indicating that substrate uses can be discretely lost or acquired during enzyme evolution. These findings exemplify how negative selection and subtle enzyme changes can lead to major evolutionary shifts in function, which can subsequently generate important adaptive advantages, for example, in improving glycolytic efficiency in Thermococcales . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments.

PubMed

Sankar, Sathish; Upadhyay, Mohita; Ramamurthy, Mageshbabu; Vadivel, Kumaran; Sagadevan, Kalaiselvan; Nandagopal, Balaji; Vivekanandan, Perumal; Sridharan, Gopalan

2015-01-01

Hantaviruses are important emerging zoonotic pathogens. The current understanding of hantavirus evolution is complicated by the lack of consensus on co-divergence of hantaviruses with their animal hosts. In addition, hantaviruses have long-term associations with their reservoir hosts. Analyzing the relative abundance of dinucleotides may shed new light on hantavirus evolution. We studied the relative abundance of dinucleotides and the evolutionary pressures shaping different hantavirus segments. A total of 118 sequences were analyzed; this includes 51 sequences of the S segment, 43 sequences of the M segment and 23 sequences of the L segment. The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed. Standard methods were used to investigate the relative roles of mutational pressure and translational selection on the three hantavirus segments. All three segments of hantaviruses are CpG depleted. Mutational pressure is the predominant evolutionary force leading to CpG depletion among hantaviruses. Interestingly, the S segment of hantaviruses is GpU depleted and in contrast to CpG depletion, the depletion of GpU dinucleotides from the S segment is driven by translational selection. Our findings also suggest that mutational pressure is the primary evolutionary pressure acting on the S and the M segments of hantaviruses. While translational selection plays a key role in shaping the evolution of the L segment. Our findings highlight how different evolutionary pressures may contribute disproportionally to the evolution of the three hantavirus segments. These findings provide new insights on the current understanding of hantavirus evolution. There is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.

Evolution of precopulatory and post-copulatory strategies of inbreeding avoidance and associated polyandry.

PubMed

Duthie, A B; Bocedi, G; Germain, R R; Reid, J M

2018-01-01

Inbreeding depression is widely hypothesized to drive adaptive evolution of precopulatory and post-copulatory mechanisms of inbreeding avoidance, which in turn are hypothesized to affect evolution of polyandry (i.e. female multiple mating). However, surprisingly little theory or modelling critically examines selection for precopulatory or post-copulatory inbreeding avoidance, or both strategies, given evolutionary constraints and direct costs, or examines how evolution of inbreeding avoidance strategies might feed back to affect evolution of polyandry. Selection for post-copulatory inbreeding avoidance, but not for precopulatory inbreeding avoidance, requires polyandry, whereas interactions between precopulatory and post-copulatory inbreeding avoidance might cause functional redundancy (i.e. 'degeneracy') potentially generating complex evolutionary dynamics among inbreeding strategies and polyandry. We used individual-based modelling to quantify evolution of interacting precopulatory and post-copulatory inbreeding avoidance and associated polyandry given strong inbreeding depression and different evolutionary constraints and direct costs. We found that evolution of post-copulatory inbreeding avoidance increased selection for initially rare polyandry and that evolution of a costly inbreeding avoidance strategy became negligible over time given a lower-cost alternative strategy. Further, fixed precopulatory inbreeding avoidance often completely precluded evolution of polyandry and hence post-copulatory inbreeding avoidance, but fixed post-copulatory inbreeding avoidance did not preclude evolution of precopulatory inbreeding avoidance. Evolution of inbreeding avoidance phenotypes and associated polyandry is therefore affected by evolutionary feedbacks and degeneracy. All else being equal, evolution of precopulatory inbreeding avoidance and resulting low polyandry is more likely when post-copulatory inbreeding avoidance is precluded or costly, and evolution of post-copulatory inbreeding avoidance greatly facilitates evolution of costly polyandry. © The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

The evolutionary outcome of sexual conflict

PubMed Central

Lessells, C(Kate). M

2006-01-01

Inter-locus sexual conflict occurs by definition when there is sexually antagonistic selection on a trait so that the optimal trait value differs between the sexes. As a result, there is selection on each sex to manipulate the trait towards its own optimum and resist such manipulation by the other sex. Sexual conflict often leads additionally to the evolution of harmful behaviour and to self-reinforcing and even perpetual sexually antagonistic coevolution. In an attempt to understand the determinants of these different outcomes, I compare two groups of traits—those related to parental investment (PI) and to mating—over which there is sexual conflict, but which have to date been explored by largely separate research traditions. A brief review suggests that sexual conflict over PI, particularly over PI per offspring, leads less frequently to the evolution of manipulative behaviour, and rarely to the evolution of harmful behaviour or to the rapid evolutionary changes which may be symptomatic of sexually antagonistic coevolution. The chief determinants of the evolutionary outcome of sexual conflict are the benefits of manipulation and resistance, the costs of manipulation and resistance, and the feasibility of manipulation. All three of these appear to contribute to the differences in the evolutionary outcome of conflicts over PI and mating. A detailed dissection of the evolutionary changes following from sexual conflict exposes greater complexity than a simple adaptation–counter-adaptation cycle and clarifies the role of harm. Not all of the evolutionary changes that follow from sexual conflict are sexually antagonistic, and harm is not necessary for sexually antagonistic coevolution to occur. In particular, whereas selection on the trait over which there is conflict is by definition sexually antagonistic, collateral harm is usually in the interest of neither sex. This creates the opportunity for palliative adaptations which reduce collateral harm. Failure to recognize that such adaptations are in the interest of both sexes can hinder our understanding of the evolutionary outcome of sexual conflict. PMID:16612889

The evolutionary outcome of sexual conflict.

PubMed

Lessells, C M

2006-02-28

Inter-locus sexual conflict occurs by definition when there is sexually antagonistic selection on a trait so that the optimal trait value differs between the sexes. As a result, there is selection on each sex to manipulate the trait towards its own optimum and resist such manipulation by the other sex. Sexual conflict often leads additionally to the evolution of harmful behaviour and to self-reinforcing and even perpetual sexually antagonistic coevolution. In an attempt to understand the determinants of these different outcomes, I compare two groups of traits-those related to parental investment (PI) and to mating-over which there is sexual conflict, but which have to date been explored by largely separate research traditions. A brief review suggests that sexual conflict over PI, particularly over PI per offspring, leads less frequently to the evolution of manipulative behaviour, and rarely to the evolution of harmful behaviour or to the rapid evolutionary changes which may be symptomatic of sexually antagonistic coevolution. The chief determinants of the evolutionary outcome of sexual conflict are the benefits of manipulation and resistance, the costs of manipulation and resistance, and the feasibility of manipulation. All three of these appear to contribute to the differences in the evolutionary outcome of conflicts over PI and mating. A detailed dissection of the evolutionary changes following from sexual conflict exposes greater complexity than a simple adaptation-counter-adaptation cycle and clarifies the role of harm. Not all of the evolutionary changes that follow from sexual conflict are sexually antagonistic, and harm is not necessary for sexually antagonistic coevolution to occur. In particular, whereas selection on the trait over which there is conflict is by definition sexually antagonistic, collateral harm is usually in the interest of neither sex. This creates the opportunity for palliative adaptations which reduce collateral harm. Failure to recognize that such adaptations are in the interest of both sexes can hinder our understanding of the evolutionary outcome of sexual conflict.

The G matrix under fluctuating correlational mutation and selection.

PubMed

Revell, Liam J

2007-08-01

Theoretical quantitative genetics provides a framework for reconstructing past selection and predicting future patterns of phenotypic differentiation. However, the usefulness of the equations of quantitative genetics for evolutionary inference relies on the evolutionary stability of the additive genetic variance-covariance matrix (G matrix). A fruitful new approach for exploring the evolutionary dynamics of G involves the use of individual-based computer simulations. Previous studies have focused on the evolution of the eigenstructure of G. An alternative approach employed in this paper uses the multivariate response-to-selection equation to evaluate the stability of G. In this approach, I measure similarity by the correlation between response-to-selection vectors due to random selection gradients. I analyze the dynamics of G under several conditions of correlational mutation and selection. As found in a previous study, the eigenstructure of G is stabilized by correlational mutation and selection. However, over broad conditions, instability of G did not result in a decreased consistency of the response to selection. I also analyze the stability of G when the correlation coefficients of correlational mutation and selection and the effective population size change through time. To my knowledge, no prior study has used computer simulations to investigate the stability of G when correlational mutation and selection fluctuate. Under these conditions, the eigenstructure of G is unstable under some simulation conditions. Different results are obtained if G matrix stability is assessed by eigenanalysis or by the response to random selection gradients. In this case, the response to selection is most consistent when certain aspects of the eigenstructure of G are least stable and vice versa.

Games of multicellularity.

PubMed

Kaveh, Kamran; Veller, Carl; Nowak, Martin A

2016-08-21

Evolutionary game dynamics are often studied in the context of different population structures. Here we propose a new population structure that is inspired by simple multicellular life forms. In our model, cells reproduce but can stay together after reproduction. They reach complexes of a certain size, n, before producing single cells again. The cells within a complex derive payoff from an evolutionary game by interacting with each other. The reproductive rate of cells is proportional to their payoff. We consider all two-strategy games. We study deterministic evolutionary dynamics with mutations, and derive exact conditions for selection to favor one strategy over another. Our main result has the same symmetry as the well-known sigma condition, which has been proven for stochastic game dynamics and weak selection. For a maximum complex size of n=2 our result holds for any intensity of selection. For n≥3 it holds for weak selection. As specific examples we study the prisoner's dilemma and hawk-dove games. Our model advances theoretical work on multicellularity by allowing for frequency-dependent interactions within groups. Copyright © 2016 Elsevier Ltd. All rights reserved.

A soul of truth in things erroneous: Popper's "amateurish" evolutionary philosophy in light of contemporary biology.

PubMed

Vecchi, Davide; Baravalle, Lorenzo

2015-01-01

This paper will critically assess Popper's evolutionary philosophy. There exists a rich literature on the topic with which we have many reservations. We believe that Popper's evolutionary philosophy should be assessed in light of the intriguing theoretical insights offered, during the last 10 years or so, by the philosophy of biology, evolutionary biology and molecular biology. We will argue that, when analysed in this manner, Popper's ideas concerning the nature of selection, Lamarckism and the theoretical limits of neo-Darwinism can be appreciated in their full biological and philosophical value.

Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics.

PubMed

Hindersin, Laura; Traulsen, Arne

2015-11-01

We analyze evolutionary dynamics on graphs, where the nodes represent individuals of a population. The links of a node describe which other individuals can be displaced by the offspring of the individual on that node. Amplifiers of selection are graphs for which the fixation probability is increased for advantageous mutants and decreased for disadvantageous mutants. A few examples of such amplifiers have been developed, but so far it is unclear how many such structures exist and how to construct them. Here, we show that almost any undirected random graph is an amplifier of selection for Birth-death updating, where an individual is selected to reproduce with probability proportional to its fitness and one of its neighbors is replaced by that offspring at random. If we instead focus on death-Birth updating, in which a random individual is removed and its neighbors compete for the empty spot, then the same ensemble of graphs consists of almost only suppressors of selection for which the fixation probability is decreased for advantageous mutants and increased for disadvantageous mutants. Thus, the impact of population structure on evolutionary dynamics is a subtle issue that will depend on seemingly minor details of the underlying evolutionary process.

Cancer Biomarkers from Genome-Scale DNA Methylation: Comparison of Evolutionary and Semantic Analysis Methods

PubMed Central

Valavanis, Ioannis; Pilalis, Eleftherios; Georgiadis, Panagiotis; Kyrtopoulos, Soterios; Chatziioannou, Aristotelis

2015-01-01

DNA methylation profiling exploits microarray technologies, thus yielding a wealth of high-volume data. Here, an intelligent framework is applied, encompassing epidemiological genome-scale DNA methylation data produced from the Illumina’s Infinium Human Methylation 450K Bead Chip platform, in an effort to correlate interesting methylation patterns with cancer predisposition and, in particular, breast cancer and B-cell lymphoma. Feature selection and classification are employed in order to select, from an initial set of ~480,000 methylation measurements at CpG sites, predictive cancer epigenetic biomarkers and assess their classification power for discriminating healthy versus cancer related classes. Feature selection exploits evolutionary algorithms or a graph-theoretic methodology which makes use of the semantics information included in the Gene Ontology (GO) tree. The selected features, corresponding to methylation of CpG sites, attained moderate-to-high classification accuracies when imported to a series of classifiers evaluated by resampling or blindfold validation. The semantics-driven selection revealed sets of CpG sites performing similarly with evolutionary selection in the classification tasks. However, gene enrichment and pathway analysis showed that it additionally provides more descriptive sets of GO terms and KEGG pathways regarding the cancer phenotypes studied here. Results support the expediency of this methodology regarding its application in epidemiological studies. PMID:27600245

Evolutionary toxicology: Meta-analysis of evolutionary events in response to chemical stressors.

PubMed

M Oziolor, Elias; De Schamphelaere, Karel; Matson, Cole W

2016-12-01

The regulatory decision-making process regarding chemical safety is most often informed by evidence based on ecotoxicity tests that consider growth, reproduction and survival as end-points, which can be quantitatively linked to short-term population outcomes. Changes in these end-points resulting from chemical exposure can cause alterations in micro-evolutionary forces (mutation, drift, selection and gene flow) that control the genetic composition of populations. With multi-generation exposures, anthropogenic contamination can lead to a population with an altered genetic composition, which may respond differently to future stressors. These evolutionary changes are rarely discussed in regulatory or risk assessment frameworks, but the growing body of literature that documents their existence suggests that these important population-level impacts should be considered. In this meta-analysis we have compared existing contamination levels of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) that have been documented to be associated with evolutionary changes in resident aquatic organisms to regulatory benchmarks for these contaminants. The original intent of this project was to perform a meta-analysis on evolutionary events associated with PCB and PAH contamination. However, this effort was hindered by a lack of consistency in congener selection for "total" PCB or PAH measurements. We expanded this manuscript to include a discussion of methods used to determine PCB and PAH total contamination in addition to comparing regulatory guidelines and contamination that has caused evolutionary effects. Micro-evolutionary responses often lead populations onto unique and unpredictable trajectories. Therefore, to better understand the risk of population-wide alterations occurring, we need to improve comparisons of chemical contamination between affected locations. In this manuscript we offer several possibilities to unify chemical comparisons for PCBs and PAHs that would improve comparability among evolutionary toxicology investigations, and with regulatory guidelines. In addition, we identify studies documenting evolutionary change in the presence of PCB and PAH contamination levels below applicable regulatory benchmarks.

Evolutionary consequences of multidriver environmental change in an aquatic primary producer.

PubMed

Brennan, Georgina L; Colegrave, Nick; Collins, Sinéad

2017-09-12

Climate change is altering aquatic environments in a complex way, and simultaneous shifts in many properties will drive evolutionary responses in primary producers at the base of both freshwater and marine ecosystems. So far, evolutionary studies have shown how changes in environmental drivers, either alone or in pairs, affect the evolution of growth and other traits in primary producers. Here, we evolve a primary producer in 96 unique environments with different combinations of between one and eight environmental drivers to understand how evolutionary responses to environmental change depend on the identity and number of drivers. Even in multidriver environments, only a few dominant drivers explain most of the evolutionary changes in population growth rates. Most populations converge on the same growth rate by the end of the evolution experiment. However, populations adapt more when these dominant drivers occur in the presence of other drivers. This is due to an increase in the intensity of selection in environments with more drivers, which are more likely to include dominant drivers. Concurrently, many of the trait changes that occur during the initial short-term response to both single and multidriver environmental change revert after about 450 generations of evolution. In future aquatic environments, populations will encounter differing combinations of drivers and intensities of selection, which will alter the adaptive potential of primary producers. Accurately gauging the intensity of selection on key primary producers will help in predicting population size and trait evolution at the base of aquatic food webs.

Learning to get along despite struggling to get by

PubMed Central

Ostrowski, Elizabeth A; Shaulsky, Gad

2009-01-01

How cooperation can evolve by natural selection is important for understanding the evolutionary transition from unicellular to multicellular life. Here we review the evolutionary theories for cooperation, with emphasis on the mechanisms that can favor cooperation and reduce conflict in multicellular organisms. PMID:19519929

What have humans done for evolutionary biology? Contributions from genes to populations.

PubMed

Briga, Michael; Griffin, Robert M; Berger, Vérane; Pettay, Jenni E; Lummaa, Virpi

2017-11-15

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future. © 2017 The Author(s).

What have humans done for evolutionary biology? Contributions from genes to populations

PubMed Central

Briga, Michael; Griffin, Robert M.; Berger, Vérane; Pettay, Jenni E.

2017-01-01

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future. PMID:29118130

Evolutionary principles and their practical application

PubMed Central

Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

2011-01-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology. PMID:25567966

Evolutionary principles and their practical application.

PubMed

Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P

2011-03-01

Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology.

Neuronal boost to evolutionary dynamics

PubMed Central

de Vladar, Harold P.; Szathmáry, Eörs

2015-01-01

Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

Environment determines evolutionary trajectory in a constrained phenotypic space

PubMed Central

Fraebel, David T; Mickalide, Harry; Schnitkey, Diane; Merritt, Jason; Kuhlman, Thomas E; Kuehn, Seppe

2017-01-01

Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select Escherichia coli for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming. In each condition parallel genomic evolution drives adaptation through different mutations. We show that the trade-off is mediated by antagonistic pleiotropy through mutations that affect negative regulation. A model of the evolutionary process shows that the genetic capacity of an organism to vary traits can qualitatively depend on its environment, which in turn alters its evolutionary trajectory. DOI: http://dx.doi.org/10.7554/eLife.24669.001 PMID:28346136

On evolutionary spatial heterogeneous games

NASA Astrophysics Data System (ADS)

Fort, H.

2008-03-01

How cooperation between self-interested individuals evolve is a crucial problem, both in biology and in social sciences, that is far from being well understood. Evolutionary game theory is a useful approach to this issue. The simplest model to take into account the spatial dimension in evolutionary games is in terms of cellular automata with just a one-parameter payoff matrix. Here, the effects of spatial heterogeneities of the environment and/or asymmetries in the interactions among the individuals are analysed through different extensions of this model. Instead of using the same universal payoff matrix, bimatrix games in which each cell at site ( i, j) has its own different ‘temptation to defect’ parameter T(i,j) are considered. First, the case in which these individual payoffs are constant in time is studied. Second, an evolving evolutionary spatial game such that T=T(i,j;t), i.e. besides depending on the position evolves (by natural selection), is used to explore the combination of spatial heterogeneity and natural selection of payoff matrices.

Are there laws of genome evolution?

PubMed

Koonin, Eugene V

2011-08-01

Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.

Eco-evolutionary effects on population recovery following catastrophic disturbance

PubMed Central

Weese, Dylan J; Schwartz, Amy K; Bentzen, Paul; Hendry, Andrew P; Kinnison, Michael T

2011-01-01

Fine-scale genetic diversity and contemporary evolution can theoretically influence ecological dynamics in the wild. Such eco-evolutionary effects might be particularly relevant to the persistence of populations facing acute or chronic environmental change. However, experimental data on wild populations is currently lacking to support this notion. One way that ongoing evolution might influence the dynamics of threatened populations is through the role that selection plays in mediating the ‘rescue effect’, the ability of migrants to contribute to the recovery of populations facing local disturbance and decline. Here, we combine experiments with natural catastrophic events to show that ongoing evolution is a major determinant of migrant contributions to population recovery in Trinidadian guppies (Poecilia reticulata). These eco-evolutionary limits on migrant contributions appear to be mediated by the reinforcing effects of natural and sexual selection against migrants, despite the close geographic proximity of migrant sources. These findings show that ongoing adaptive evolution can be a double-edged sword for population persistence, maintaining local fitness at a cost to demographic risk. Our study further serves as a potent reminder that significant evolutionary and eco-evolutionary dynamics might be at play even where the phenotypic status quo is largely maintained generation to generation. PMID:25567978

Darwinian natural selection: its enduring explanatory power

PubMed Central

2012-01-01

Evolutionary theory has never had a stronger scientific foundation than it does today. In a short review I hope to portray the deep commitment of today's biologists to Darwinian natural selection and to discoveries made since Darwin's time. In spite of the scientific advances in the century and a half since the publication of On the Origin of Species, Darwin still remains the principal author of modern evolutionary theory. He is one of the greatest contributors of all time to our understanding of nature. PMID:22481845

Phylogenetic inertia and Darwin's higher law.

PubMed

Shanahan, Timothy

2011-03-01

The concept of 'phylogenetic inertia' is routinely deployed in evolutionary biology as an alternative to natural selection for explaining the persistence of characteristics that appear sub-optimal from an adaptationist perspective. However, in many of these contexts the precise meaning of 'phylogenetic inertia' and its relationship to selection are far from clear. After tracing the history of the concept of 'inertia' in evolutionary biology, I argue that treating phylogenetic inertia and natural selection as alternative explanations is mistaken because phylogenetic inertia is, from a Darwinian point of view, simply an expected effect of selection. Although Darwin did not discuss 'phylogenetic inertia,' he did assert the explanatory priority of selection over descent. An analysis of 'phylogenetic inertia' provides a perspective from which to assess Darwin's view. Copyright © 2010 Elsevier Ltd. All rights reserved.

Evolutionary dynamics on graphs: Efficient method for weak selection

NASA Astrophysics Data System (ADS)

Fu, Feng; Wang, Long; Nowak, Martin A.; Hauert, Christoph

2009-04-01

Investigating the evolutionary dynamics of game theoretical interactions in populations where individuals are arranged on a graph can be challenging in terms of computation time. Here, we propose an efficient method to study any type of game on arbitrary graph structures for weak selection. In this limit, evolutionary game dynamics represents a first-order correction to neutral evolution. Spatial correlations can be empirically determined under neutral evolution and provide the basis for formulating the game dynamics as a discrete Markov process by incorporating a detailed description of the microscopic dynamics based on the neutral correlations. This framework is then applied to one of the most intriguing questions in evolutionary biology: the evolution of cooperation. We demonstrate that the degree heterogeneity of a graph impedes cooperation and that the success of tit for tat depends not only on the number of rounds but also on the degree of the graph. Moreover, considering the mutation-selection equilibrium shows that the symmetry of the stationary distribution of states under weak selection is skewed in favor of defectors for larger selection strengths. In particular, degree heterogeneity—a prominent feature of scale-free networks—generally results in a more pronounced increase in the critical benefit-to-cost ratio required for evolution to favor cooperation as compared to regular graphs. This conclusion is corroborated by an analysis of the effects of population structures on the fixation probabilities of strategies in general 2×2 games for different types of graphs. Computer simulations confirm the predictive power of our method and illustrate the improved accuracy as compared to previous studies.

Local population density and group composition influence the signal-preference relationship in Enchenopa treehoppers (Hemiptera: Membracidae).

PubMed

Fowler-Finn, K D; Cruz, D C; Rodríguez, R L

2017-01-01

Many animals exhibit social plasticity - changes in phenotype or behaviour in response to experience with conspecifics that change how evolutionary processes like sexual selection play out. Here, we asked whether social plasticity arising from variation in local population density in male advertisement signals and female mate preferences influences the form of sexual selection. We manipulated local density and determined whether this changed how the distribution of male signals overlapped with female preferences - the signal preference relationship. We specifically look at the shape of female mate preference functions, which, when compared to signal distributions, provide hypotheses about the form of sexual selection. We used Enchenopa binotata treehoppers, a group of plant-feeding insects that exhibit natural variation in local densities across individual host plants, populations, species and years. We measured male signal frequency and female preference functions across the density treatments. We found that male signals varied across local social groups, but not according to local density. By contrast, female preferences varied with local density - favouring higher signal frequencies in denser environments. Thus, local density changes the signal-preference relationship and, consequently, the expected form of sexual selection. We found no influence of sex ratio on the signal-preference relationship. Our findings suggest that plasticity arising from variation in local group density and composition can alter the form of sexual selection with potentially important consequences both for the maintenance of variation and for speciation. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Plant Minders

NASA Technical Reports Server (NTRS)

1988-01-01

Indoor plants are automatically watered by the Aqua Trends watering system. System draws water from building outlets or from pump/reservoir module and distributes it to the plants via a network of tubes and adjustable nozzles. Key element of system is electronic controller programmed to dispense water according to the needs of various plants in an installation. Adjustable nozzle meters out exactly right amount of water at proper time to the plant it's serving. More than 100 Aqua/Trends systems are in service in the USA, from a simple residential system to a large Mirage III system integrated to water all greenery in a large office or apartment building.

Determining the Intensity of a Point-Like Source Observed on the Background of AN Extended Source

NASA Astrophysics Data System (ADS)

Kornienko, Y. V.; Skuratovskiy, S. I.

2014-12-01

The problem of determining the time dependence of intensity of a point-like source in case of atmospheric blur is formulated and solved by using the Bayesian statistical approach. A pointlike source is supposed to be observed on the background of an extended source with constant in time though unknown brightness. The equation system for optimal statistical estimation of the sequence of intensity values in observation moments is obtained. The problem is particularly relevant for studying gravitational mirages which appear while observing a quasar through the gravitational field of a far galaxy.

Unsteady aerodynamic characterization of a military aircraft in vertical gusts

NASA Technical Reports Server (NTRS)

Lebozec, A.; Cocquerez, J. L.

1985-01-01

The effects of 2.5-m/sec vertical gusts on the flight characteristics of a 1:8.6 scale model of a Mirage 2000 aircraft in free flight at 35 m/sec over a distance of 30 m are investigated. The wind-tunnel setup and instrumentation are described; the impulse-response and local-coefficient-identification analysis methods applied are discussed in detail; and the modification and calibration of the gust-detection probes are reviewed. The results are presented in graphs, and good general agreement is obtained between model calculations using the two analysis methods and the experimental measurements.

Evolution in Mind: Evolutionary Dynamics, Cognitive Processes, and Bayesian Inference.

PubMed

Suchow, Jordan W; Bourgin, David D; Griffiths, Thomas L

2017-07-01

Evolutionary theory describes the dynamics of population change in settings affected by reproduction, selection, mutation, and drift. In the context of human cognition, evolutionary theory is most often invoked to explain the origins of capacities such as language, metacognition, and spatial reasoning, framing them as functional adaptations to an ancestral environment. However, evolutionary theory is useful for understanding the mind in a second way: as a mathematical framework for describing evolving populations of thoughts, ideas, and memories within a single mind. In fact, deep correspondences exist between the mathematics of evolution and of learning, with perhaps the deepest being an equivalence between certain evolutionary dynamics and Bayesian inference. This equivalence permits reinterpretation of evolutionary processes as algorithms for Bayesian inference and has relevance for understanding diverse cognitive capacities, including memory and creativity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolution in population parameters: density-dependent selection or density-dependent fitness?

PubMed

Travis, Joseph; Leips, Jeff; Rodd, F Helen

2013-05-01

Density-dependent selection is one of earliest topics of joint interest to both ecologists and evolutionary biologists and thus occupies an important position in the histories of these disciplines. This joint interest is driven by the fact that density-dependent selection is the simplest form of feedback between an ecological effect of an organism's own making (crowding due to sustained population growth) and the selective response to the resulting conditions. This makes density-dependent selection perhaps the simplest process through which we see the full reciprocity between ecology and evolution. In this article, we begin by tracing the history of studying the reciprocity between ecology and evolution, which we see as combining the questions of evolutionary ecology with the assumptions and approaches of ecological genetics. In particular, density-dependent fitness and density-dependent selection were critical concepts underlying ideas about adaptation to biotic selection pressures and the coadaptation of interacting species. However, theory points to a critical distinction between density-dependent fitness and density-dependent selection in their influences on complex evolutionary and ecological interactions among coexisting species. Although density-dependent fitness is manifestly evident in empirical studies, evidence of density-dependent selection is much less common. This leads to the larger question of how prevalent and important density-dependent selection might really be. Life-history variation in the least killifish Heterandria formosa appears to reflect the action of density-dependent selection, and yet compelling evidence is elusive, even in this well-studied system, which suggests some important challenges for understanding density-driven feedbacks between ecology and evolution.

Genomic signature of natural and anthropogenic stress in wild populations of the waterflea Daphnia magna: validation in space, time and experimental evolution.

PubMed

Orsini, Luisa; Spanier, Katina I; DE Meester, Luc

2012-05-01

Natural populations are confronted with multiple selection pressures resulting in a mosaic of environmental stressors at the landscape level. Identifying the genetic underpinning of adaptation to these complex selection environments and assigning causes of natural selection within multidimensional selection regimes in the wild is challenging. The water flea Daphnia is a renowned ecological model system with its well-documented ecology, the possibility to analyse subfossil dormant egg banks and the short generation time allowing an experimental evolution approach. Capitalizing on the strengths of this model system, we here link candidate genome regions to three selection pressures, known to induce micro-evolutionary responses in Daphnia magna: fish predation, parasitism and land use. Using a genome scan approach in space, time and experimental evolution trials, we provide solid evidence of selection at the genome level under well-characterized environmental gradients in the wild and identify candidate genes linked to the three environmental stressors. Our study reveals differential selection at the genome level in Daphnia populations and provides evidence for repeatable patterns of local adaptation in a geographic mosaic of environmental stressors fuelled by standing genetic variation. Our results imply high evolutionary potential of local populations, which is relevant to understand the dynamics of trait changes in natural populations and their impact on community and ecosystem responses through eco-evolutionary feedbacks. © 2012 Blackwell Publishing Ltd.

It's a bear market: evolutionary and ecological effects of predation on two wild sockeye salmon populations

PubMed Central

Lin, J E; Hard, J J; Naish, K A; Peterson, D; Hilborn, R; Hauser, L

2016-01-01

Predation can affect both phenotypic variation and population productivity in the wild, but quantifying evolutionary and demographic effects of predation in natural environments is challenging. The aim of this study was to estimate selection differentials and coefficients associated with brown bear (Ursus arctos) predation in wild sockeye salmon (Oncorhynchus nerka) populations spawning in pristine habitat that is often subject to intense predation pressure. Using reconstructed genetic pedigrees, individual reproductive success (RS) was estimated in two sockeye salmon populations for two consecutive brood years with very different predation intensities across brood years. Phenotypic data on individual adult body length, body depth, stream entry timing and reproductive lifespan were used to calculate selection coefficients based on RS, and genetic variance components were estimated using animal models. Bears consistently killed larger and more recently arrived adults, although selection differentials were small. In both populations, mean RS was higher in the brood year experiencing lower predation intensity. Selection coefficients were similar across brood years with different levels of predation, often indicating stabilizing selection on reproductive lifespan as well as directional selection for longer reproductive lifespan. Despite these selection pressures, genetic covariation of morphology, phenology and lifespan appears to have maintained variation in spawner body size and stream entry timing in both populations. Our results therefore suggest considerable demographic but limited evolutionary effects of bear predation in the two study populations. PMID:26860201

It's a bear market: evolutionary and ecological effects of predation on two wild sockeye salmon populations.

PubMed

Lin, J E; Hard, J J; Naish, K A; Peterson, D; Hilborn, R; Hauser, L

2016-05-01

Predation can affect both phenotypic variation and population productivity in the wild, but quantifying evolutionary and demographic effects of predation in natural environments is challenging. The aim of this study was to estimate selection differentials and coefficients associated with brown bear (Ursus arctos) predation in wild sockeye salmon (Oncorhynchus nerka) populations spawning in pristine habitat that is often subject to intense predation pressure. Using reconstructed genetic pedigrees, individual reproductive success (RS) was estimated in two sockeye salmon populations for two consecutive brood years with very different predation intensities across brood years. Phenotypic data on individual adult body length, body depth, stream entry timing and reproductive lifespan were used to calculate selection coefficients based on RS, and genetic variance components were estimated using animal models. Bears consistently killed larger and more recently arrived adults, although selection differentials were small. In both populations, mean RS was higher in the brood year experiencing lower predation intensity. Selection coefficients were similar across brood years with different levels of predation, often indicating stabilizing selection on reproductive lifespan as well as directional selection for longer reproductive lifespan. Despite these selection pressures, genetic covariation of morphology, phenology and lifespan appears to have maintained variation in spawner body size and stream entry timing in both populations. Our results therefore suggest considerable demographic but limited evolutionary effects of bear predation in the two study populations.

A novel method of comparing mating success and survival reveals similar sexual and viability selection for mobility traits in female tree crickets.

PubMed

Ercit, K; Gwynne, D T

2016-06-01

The relationship between sexual and viability selection in females is necessarily different than that in males, as investment in sexual traits potentially comes at the expense of both fecundity and survival. Accordingly, females do not usually invest in sexually selected traits. However, direct benefits obtained from mating, such as nuptial gifts, may encourage competition among females and subsidize investment into sexually selected traits. We compared sexual and viability selection on female tree crickets Oecanthus nigricornis, a species where females mate frequently to obtain nuptial gifts and sexual selection on females is likely. If male choice determines female mating success in this species, we expect sexual selection for fecundity traits, as males of many species prefer more fecund females. Alternatively, intrasexual scramble or combat competition on females may select for larger jumping legs or wider heads (respectively). We estimated mating success in wild caught crickets using microsatellite analysis of stored sperm and estimated relative viability by comparing surviving female O. nigricornis to those captured by a common wasp predator. In support of the scramble competition hypothesis, we found sexual selection for females with larger hind legs and narrower heads. We also found stabilizing viability selection for intermediate head width and hind leg size. As predicted, traits under viability and sexual selection were very similar, and the direction of that selection was not opposing. However, because the shape of sexual and viability selection differs, these episodes of selection may favour slightly different trait sizes. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

How evolutionary principles improve the understanding of human health and disease.

PubMed

Gluckman, Peter D; Low, Felicia M; Buklijas, Tatjana; Hanson, Mark A; Beedle, Alan S

2011-03-01

An appreciation of the fundamental principles of evolutionary biology provides new insights into major diseases and enables an integrated understanding of human biology and medicine. However, there is a lack of awareness of their importance amongst physicians, medical researchers, and educators, all of whom tend to focus on the mechanistic (proximate) basis for disease, excluding consideration of evolutionary (ultimate) reasons. The key principles of evolutionary medicine are that selection acts on fitness, not health or longevity; that our evolutionary history does not cause disease, but rather impacts on our risk of disease in particular environments; and that we are now living in novel environments compared to those in which we evolved. We consider these evolutionary principles in conjunction with population genetics and describe several pathways by which evolutionary processes can affect disease risk. These perspectives provide a more cohesive framework for gaining insights into the determinants of health and disease. Coupled with complementary insights offered by advances in genomic, epigenetic, and developmental biology research, evolutionary perspectives offer an important addition to understanding disease. Further, there are a number of aspects of evolutionary medicine that can add considerably to studies in other domains of contemporary evolutionary studies.

How evolutionary principles improve the understanding of human health and disease

PubMed Central

Gluckman, Peter D; Low, Felicia M; Buklijas, Tatjana; Hanson, Mark A; Beedle, Alan S

2011-01-01

An appreciation of the fundamental principles of evolutionary biology provides new insights into major diseases and enables an integrated understanding of human biology and medicine. However, there is a lack of awareness of their importance amongst physicians, medical researchers, and educators, all of whom tend to focus on the mechanistic (proximate) basis for disease, excluding consideration of evolutionary (ultimate) reasons. The key principles of evolutionary medicine are that selection acts on fitness, not health or longevity; that our evolutionary history does not cause disease, but rather impacts on our risk of disease in particular environments; and that we are now living in novel environments compared to those in which we evolved. We consider these evolutionary principles in conjunction with population genetics and describe several pathways by which evolutionary processes can affect disease risk. These perspectives provide a more cohesive framework for gaining insights into the determinants of health and disease. Coupled with complementary insights offered by advances in genomic, epigenetic, and developmental biology research, evolutionary perspectives offer an important addition to understanding disease. Further, there are a number of aspects of evolutionary medicine that can add considerably to studies in other domains of contemporary evolutionary studies. PMID:25567971

Evolution of complex life cycles in trophically transmitted helminths. I. Host incorporation and trophic ascent.

PubMed

Parker, G A; Ball, M A; Chubb, J C

2015-02-01

Links between parasites and food webs are evolutionarily ancient but dynamic: life history theory provides insights into helminth complex life cycle origins. Most adult helminths benefit by sexual reproduction in vertebrates, often high up food chains, but direct infection is commonly constrained by a trophic vacuum between free-living propagules and definitive hosts. Intermediate hosts fill this vacuum, facilitating transmission to definitive hosts. The central question concerns why sexual reproduction, and sometimes even larval growth, is suppressed in intermediate hosts, favouring growth arrest at larval maturity in intermediate hosts and reproductive suppression until transmission to definitive hosts? Increased longevity and higher growth in definitive hosts can generate selection for larger parasite body size and higher fecundity at sexual maturity. Life cycle length is increased by two evolutionary mechanisms, upward and downward incorporation, allowing simple (one-host) cycles to become complex (multihost). In downward incorporation, an intermediate host is added below the definitive host: models suggest that downward incorporation probably evolves only after ecological or evolutionary perturbations create a trophic vacuum. In upward incorporation, a new definitive host is added above the original definitive host, which subsequently becomes an intermediate host, again maintained by the trophic vacuum: theory suggests that this is plausible even under constant ecological/evolutionary conditions. The final cycle is similar irrespective of its origin (upward or downward). Insights about host incorporation are best gained by linking comparative phylogenetic analyses (describing evolutionary history) with evolutionary models (examining selective forces). Ascent of host trophic levels and evolution of optimal host taxa ranges are discussed. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes

PubMed Central

Kohli, Gurjeet S; John, Uwe; Van Dolah, Frances M; Murray, Shauna A

2016-01-01

Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success. PMID:26784357

Fixation of competing strategies when interacting agents differ in the time scale of strategy updating

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Weissing, Franz J.; Cao, Ming

2016-09-01

A commonly used assumption in evolutionary game theory is that natural selection acts on individuals in the same time scale; e.g., players use the same frequency to update their strategies. Variation in learning rates within populations suggests that evolutionary game theory may not necessarily be restricted to uniform time scales associated with the game interaction and strategy adaption evolution. In this study, we remove this restricting assumption by dividing the population into fast and slow groups according to the players' strategy updating frequencies and investigate how different strategy compositions of one group influence the evolutionary outcome of the other's fixation probabilities of strategies within its own group. Analytical analysis and numerical calculations are performed to study the evolutionary dynamics of strategies in typical classes of two-player games (prisoner's dilemma game, snowdrift game, and stag-hunt game). The introduction of the heterogeneity in strategy-update time scales leads to substantial changes in the evolution dynamics of strategies. We provide an approximation formula for the fixation probability of mutant types in finite populations and study the outcome of strategy evolution under the weak selection. We find that although heterogeneity in time scales makes the collective evolutionary dynamics more complicated, the possible long-run evolutionary outcome can be effectively predicted under technical assumptions when knowing the population composition and payoff parameters.

Capability of the Maximax&Maximin selection operator in the evolutionary algorithm for a nurse scheduling problem

NASA Astrophysics Data System (ADS)

Ramli, Razamin; Tein, Lim Huai

2016-08-01

A good work schedule can improve hospital operations by providing better coverage with appropriate staffing levels in managing nurse personnel. Hence, constructing the best nurse work schedule is the appropriate effort. In doing so, an improved selection operator in the Evolutionary Algorithm (EA) strategy for a nurse scheduling problem (NSP) is proposed. The smart and efficient scheduling procedures were considered. Computation of the performance of each potential solution or schedule was done through fitness evaluation. The best so far solution was obtained via special Maximax&Maximin (MM) parent selection operator embedded in the EA, which fulfilled all constraints considered in the NSP.

Clownfishes evolution below and above the species level

PubMed Central

Litsios, Glenn; Faye, Laurélène; Salamin, Nicolas

2018-01-01

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels. PMID:29467260

Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.

PubMed

Moncla, Louise H; Zhong, Gongxun; Nelson, Chase W; Dinis, Jorge M; Mutschler, James; Hughes, Austin L; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C

2016-02-10

Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses. Copyright © 2016 Elsevier Inc. All rights reserved.

Adaptive Topographies and Equilibrium Selection in an Evolutionary Game

PubMed Central

Osinga, Hinke M.; Marshall, James A. R.

2015-01-01

It has long been known in the field of population genetics that adaptive topographies, in which population equilibria maximise mean population fitness for a trait regardless of its genetic bases, do not exist. Whether one chooses to model selection acting on a single locus or multiple loci does matter. In evolutionary game theory, analysis of a simple and general game involving distinct roles for the two players has shown that whether strategies are modelled using a single ‘locus’ or one ‘locus’ for each role, the stable population equilibria are unchanged and correspond to the fitness-maximising evolutionary stable strategies of the game. This is curious given the aforementioned population genetical results on the importance of the genetic bases of traits. Here we present a dynamical systems analysis of the game with roles detailing how, while the stable equilibria in this game are unchanged by the number of ‘loci’ modelled, equilibrium selection may differ under the two modelling approaches. PMID:25706762

Product Mix Selection Using AN Evolutionary Technique

NASA Astrophysics Data System (ADS)

Tsoulos, Ioannis G.; Vasant, Pandian

2009-08-01

This paper proposes an evolutionary technique for the solution of a real—life industrial problem and particular for the product mix selection problem. The evolutionary technique is a combination of a genetic algorithm that preserves the feasibility of the trial solutions with penalties and some local optimization method. The goal of this paper has been achieved in finding the best near optimal solution for the profit fitness function respect to vagueness factor and level of satisfaction. The findings of the profit values will be very useful for the decision makers in the industrial engineering sector for the implementation purpose. It's possible to improve the solutions obtained in this study by employing other meta-heuristic methods such as simulated annealing, tabu Search, ant colony optimization, particle swarm optimization and artificial immune systems.

The eco-evolutionary impacts of domestication and agricultural practices on wild species.

PubMed

Turcotte, Martin M; Araki, Hitoshi; Karp, Daniel S; Poveda, Katja; Whitehead, Susan R

2017-01-19

Agriculture is a dominant evolutionary force that drives the evolution of both domesticated and wild species. However, the various mechanisms of agriculture-induced evolution and their socio-ecological consequences are not often synthetically discussed. Here, we explore how agricultural practices and evolutionary changes in domesticated species cause evolution in wild species. We do so by examining three processes by which agriculture drives evolution. First, differences in the traits of domesticated species, compared with their wild ancestors, alter the selective environment and create opportunities for wild species to specialize. Second, selection caused by agricultural practices, including both those meant to maximize productivity and those meant to control pest species, can lead to pest adaptation. Third, agriculture can cause non-selective changes in patterns of gene flow in wild species. We review evidence for these processes and then discuss their ecological and sociological impacts. We finish by identifying important knowledge gaps and future directions related to the eco-evolutionary impacts of agriculture including their extent, how to prevent the detrimental evolution of wild species, and finally, how to use evolution to minimize the ecological impacts of agriculture.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

The eco-evolutionary impacts of domestication and agricultural practices on wild species

PubMed Central

Araki, Hitoshi; Karp, Daniel S.; Poveda, Katja

2017-01-01

Agriculture is a dominant evolutionary force that drives the evolution of both domesticated and wild species. However, the various mechanisms of agriculture-induced evolution and their socio-ecological consequences are not often synthetically discussed. Here, we explore how agricultural practices and evolutionary changes in domesticated species cause evolution in wild species. We do so by examining three processes by which agriculture drives evolution. First, differences in the traits of domesticated species, compared with their wild ancestors, alter the selective environment and create opportunities for wild species to specialize. Second, selection caused by agricultural practices, including both those meant to maximize productivity and those meant to control pest species, can lead to pest adaptation. Third, agriculture can cause non-selective changes in patterns of gene flow in wild species. We review evidence for these processes and then discuss their ecological and sociological impacts. We finish by identifying important knowledge gaps and future directions related to the eco-evolutionary impacts of agriculture including their extent, how to prevent the detrimental evolution of wild species, and finally, how to use evolution to minimize the ecological impacts of agriculture. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’. PMID:27920378

An evolutionary algorithm for large traveling salesman problems.

PubMed

Tsai, Huai-Kuang; Yang, Jinn-Moon; Tsai, Yuan-Fang; Kao, Cheng-Yan

2004-08-01

This work proposes an evolutionary algorithm, called the heterogeneous selection evolutionary algorithm (HeSEA), for solving large traveling salesman problems (TSP). The strengths and limitations of numerous well-known genetic operators are first analyzed, along with local search methods for TSPs from their solution qualities and mechanisms for preserving and adding edges. Based on this analysis, a new approach, HeSEA is proposed which integrates edge assembly crossover (EAX) and Lin-Kernighan (LK) local search, through family competition and heterogeneous pairing selection. This study demonstrates experimentally that EAX and LK can compensate for each other's disadvantages. Family competition and heterogeneous pairing selections are used to maintain the diversity of the population, which is especially useful for evolutionary algorithms in solving large TSPs. The proposed method was evaluated on 16 well-known TSPs in which the numbers of cities range from 318 to 13509. Experimental results indicate that HeSEA performs well and is very competitive with other approaches. The proposed method can determine the optimum path when the number of cities is under 10,000 and the mean solution quality is within 0.0074% above the optimum for each test problem. These findings imply that the proposed method can find tours robustly with a fixed small population and a limited family competition length in reasonable time, when used to solve large TSPs.

Multivariate sexual selection on male tegmina in wild populations of sagebrush crickets, Cyphoderris strepitans (Orthoptera: Haglidae).

PubMed

Ower, G D; Hunt, J; Sakaluk, S K

2017-02-01

Although the strength and form of sexual selection on song in male crickets have been studied extensively, few studies have examined selection on the morphological structures that underlie variation in males' song, particularly in wild populations. Geometric morphometric techniques were used to measure sexual selection on the shape, size and symmetry of both top and bottom tegmina in wild populations of sagebrush crickets, a species in which nuptial feeding by females imposes an unambiguous phenotypic marker on males. The size of the tegmina negatively covaried with song dominant frequency and positively covaried with song pulse duration. Sexual selection was more intense on the bottom tegmen, conceivably because it interacts more freely with the subtegminal airspace, which may play a role in song amplification. An expanded coastal/subcostal region was one of the phenotypes strongly favoured by disruptive selection on the bottom tegmen, an adaptation that may form a more effective seal with the thorax to prevent noise cancellation. Directional selection also favoured increased symmetry in tegminal shape. Assuming more symmetrical males are better able to buffer against developmental noise, the song produced by these males may make them more attractive to females. Despite the strong stabilizing selection documented previously on the dominant frequency of the song, stabilizing selection on the resonator that regulates dominant frequency was surprisingly absent. Nonetheless, wing morphology had an important influence on song structure and appears to be subject to significant linear and nonlinear sexual selection through female mate choice. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Sex-ratio control erodes sexual selection, revealing evolutionary feedback from adaptive plasticity.

PubMed

Fawcett, Tim W; Kuijper, Bram; Weissing, Franz J; Pen, Ido

2011-09-20

Female choice is a powerful selective force, driving the elaboration of conspicuous male ornaments. This process of sexual selection has profound implications for many life-history decisions, including sex allocation. For example, females with attractive partners should produce more sons, because these sons will inherit their father's attractiveness and enjoy high mating success, thereby yielding greater fitness returns than daughters. However, previous research has overlooked the fact that there is a reciprocal feedback from life-history strategies to sexual selection. Here, using a simple mathematical model, we show that if mothers adaptively control offspring sex in relation to their partner's attractiveness, sexual selection is weakened and male ornamentation declines. This weakening occurs because the ability to determine offspring sex reduces the fitness difference between females with attractive and unattractive partners. We use individual-based, evolutionary simulations to show that this result holds under more biologically realistic conditions. Sexual selection and sex allocation thus interact in a dynamic fashion: The evolution of conspicuous male ornaments favors sex-ratio adjustment, but this conditional strategy then undermines the very same process that generated it, eroding sexual selection. We predict that, all else being equal, the most elaborate sexual displays should be seen in species with little or no control over offspring sex. The feedback process we have described points to a more general evolutionary principle, in which a conditional strategy weakens directional selection on another trait by reducing fitness differences.

Fluctuating selection: the perpetual renewal of adaptation in variable environments

PubMed Central

Bell, Graham

2010-01-01

Darwin insisted that evolutionary change occurs very slowly over long periods of time, and this gradualist view was accepted by his supporters and incorporated into the infinitesimal model of quantitative genetics developed by R. A. Fisher and others. It dominated the first century of evolutionary biology, but has been challenged in more recent years both by field surveys demonstrating strong selection in natural populations and by quantitative trait loci and genomic studies, indicating that adaptation is often attributable to mutations in a few genes. The prevalence of strong selection seems inconsistent, however, with the high heritability often observed in natural populations, and with the claim that the amount of morphological change in contemporary and fossil lineages is independent of elapsed time. I argue that these discrepancies are resolved by realistic accounts of environmental and evolutionary changes. First, the physical and biotic environment varies on all time-scales, leading to an indefinite increase in environmental variance over time. Secondly, the intensity and direction of natural selection are also likely to fluctuate over time, leading to an indefinite increase in phenotypic variance in any given evolving lineage. Finally, detailed long-term studies of selection in natural populations demonstrate that selection often changes in direction. I conclude that the traditional gradualist scheme of weak selection acting on polygenic variation should be supplemented by the view that adaptation is often based on oligogenic variation exposed to commonplace, strong, fluctuating natural selection. PMID:20008388

Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India.

PubMed

Lewnard, Joseph A; Townsend, Jeffrey P

2016-12-20

Immune heterogeneity in wild host populations indicates that disease-mediated selection is common in nature. However, the underlying dynamic feedbacks involving the ecology of disease transmission, evolutionary processes, and their interaction with environmental drivers have proven challenging to characterize. Plague presents an optimal system for interrogating such couplings: Yersinia pestis transmission exerts intense selective pressure driving the local persistence of disease resistance among its wildlife hosts in endemic areas. Investigations undertaken in colonial India after the introduction of plague in 1896 suggest that, only a decade after plague arrived, a heritable, plague-resistant phenotype had become prevalent among commensal rats of cities undergoing severe plague epidemics. To understand the possible evolutionary basis of these observations, we developed a mathematical model coupling environmentally forced plague dynamics with evolutionary selection of rats, capitalizing on extensive archival data from Indian Plague Commission investigations. Incorporating increased plague resistance among rats as a consequence of intense natural selection permits the model to reproduce observed changes in seasonal epidemic patterns in several cities and capture experimentally observed associations between climate and flea population dynamics in India. Our model results substantiate Victorian era claims of host evolution based on experimental observations of plague resistance and reveal the buffering effect of such evolution against environmental drivers of transmission. Our analysis shows that historical datasets can yield powerful insights into the transmission dynamics of reemerging disease agents with which we have limited contemporary experience to guide quantitative modeling and inference.

Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India

PubMed Central

Lewnard, Joseph A.

2016-01-01

Immune heterogeneity in wild host populations indicates that disease-mediated selection is common in nature. However, the underlying dynamic feedbacks involving the ecology of disease transmission, evolutionary processes, and their interaction with environmental drivers have proven challenging to characterize. Plague presents an optimal system for interrogating such couplings: Yersinia pestis transmission exerts intense selective pressure driving the local persistence of disease resistance among its wildlife hosts in endemic areas. Investigations undertaken in colonial India after the introduction of plague in 1896 suggest that, only a decade after plague arrived, a heritable, plague-resistant phenotype had become prevalent among commensal rats of cities undergoing severe plague epidemics. To understand the possible evolutionary basis of these observations, we developed a mathematical model coupling environmentally forced plague dynamics with evolutionary selection of rats, capitalizing on extensive archival data from Indian Plague Commission investigations. Incorporating increased plague resistance among rats as a consequence of intense natural selection permits the model to reproduce observed changes in seasonal epidemic patterns in several cities and capture experimentally observed associations between climate and flea population dynamics in India. Our model results substantiate Victorian era claims of host evolution based on experimental observations of plague resistance and reveal the buffering effect of such evolution against environmental drivers of transmission. Our analysis shows that historical datasets can yield powerful insights into the transmission dynamics of reemerging disease agents with which we have limited contemporary experience to guide quantitative modeling and inference. PMID:27791071

Dynamic selective environments and evolutionary traps in human-dominated landscapes.

PubMed

Rodewald, Amanda D; Shustack, Daniel P; Jones, Todd M

2011-09-01

Human activities can alter selective environments in ways that can reduce the usefulness of certain ornamental traits as honest signals of individual quality and, in some cases, may create evolutionary traps, where rapid changes in selective environments result in maladaptive behavioral decisions. Using the sexually dichromatic, socially monogamous Northern Cardinal (Cardinalis cardinalis) as a model, we hypothesized that urbanization would erode the relationship between plumage coloration and reproductive success. Because the exotic Amur honeysuckle (Lonicera maackii) provides carotenoids, is a preferred habitat attribute, and increases vulnerability to nest predation, we predicted the presence of an evolutionary trap, whereby the brightest males would achieve the lowest reproductive success. Working at 14 forests in Ohio, USA, 2006-2008, we measured plumage color, monitored reproduction, and quantified habitat within territories. In rural landscapes, the brightest males bred earliest in the season and secured more preferred territories; however, annual reproduction declined with plumage brightness. Coloration of urban males was not associated with territory attributes or reproduction. Female redness across all landscapes was negatively related to reproduction. Poor reproductive performance of otherwise higher-quality males probably resulted from preferences for honeysuckle, which reduces annual reproduction when used as a nesting substrate early in the season. In this way, exotic shrubs prompted an evolutionary trap that was avoided in urban forests where anthropogenic resources disassociated male color and reproductive phenology and success. Our study illustrates how modified selective environments in human-dominated landscapes might shape microevolutionary processes in wild bird populations.

Ecological genetics of sediment browsing behaviour in a planktonic crustacean.

PubMed

Arbore, R; Andras, J P; Routtu, J; Ebert, D

2016-10-01

Zooplankton can display complex habitat selection behaviours that influence the way they interact with their environments. Some species, although primarily pelagic, can exploit sediment-borne particles as a food source or use sediments as a refuge from pelagic predation. However, this strategy may increase the exposure to other risks such as benthic predation and infection from sediment-borne parasite transmission stages. The evolution of habitat selection behaviour in these species is thus expected to be influenced by multiple and possibly contrasting selective forces. Here, we study the browsing behaviour of the water flea Daphnia magna on bottom sediments. First, we demonstrated genetic variation for sediment browsing among D. magna genotypes from natural populations sampled across a broad geographic range. Next, we used an F2 recombinant panel to perform a QTL analysis and identified three regions in the D. magna genome contributing to variation in browsing behaviour. We also analysed the correlation between our data and previously published data on the phototactic behaviour of genotypes from the same F2 panel. Clonal means of the two behavioral traits were not correlated, suggesting that they may evolve independently. Browsing behaviour is likely to be a relevant component of habitat selection in D. magna, and its study may help to incorporate the interactions with the sediment into eco-evolutionary models of this key freshwater species. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Correlated evolution of personality, morphology and performance

PubMed Central

Kern, Elizabeth M. A.; Robinson, Detric; Gass, Erika; Godwin, John; Langerhans, R. Brian

2018-01-01

Evolutionary change in one trait can elicit evolutionary changes in other traits due to genetic correlations. This constrains the independent evolution of traits and can lead to unpredicted ecological and evolutionary outcomes. Animals might frequently exhibit genetic associations among behavioural and morphological-physiological traits, because the physiological mechanisms behind animal personality can have broad multitrait effects and because many selective agents influence the evolution of multiple types of traits. However, we currently know little about genetic correlations between animal personalities and nonbehavioural traits. We tested for associations between personality, morphology and locomotor performance by comparing zebrafish (Danio rerio) collected from the wild and then selectively bred for either a proactive or reactive stress coping style (‘bold’ or ‘shy’ phenotypes). Based on adaptive hypotheses of correlational selection in the wild, we predicted that artificial selection for boldness would produce correlated evolutionary responses of larger caudal regions and higher fast-start escape performance (and the opposite for shyness). After four to seven generations, morphology and locomotor performance differed between personality lines: bold zebrafish exhibited a larger caudal region and higher fast-start performance than fish in the shy line, matching predictions. Individual-level phenotypic correlations suggested that pleiotropy or physical gene linkage likely explained the correlated response of locomotor performance, while the correlated response of body shape may have reflected linkage disequilibrium, which is breaking down each generation in the laboratory. Our results indicate that evolution of personality can result in concomitant changes in morphology and whole-organism performance, and vice versa. PMID:29398712

How cancer shapes evolution, and how evolution shapes cancer

PubMed Central

Casás-Selves, Matias; DeGregori, James

2013-01-01

Evolutionary theories are critical for understanding cancer development at the level of species as well as at the level of cells and tissues, and for developing effective therapies. Animals have evolved potent tumor suppressive mechanisms to prevent cancer development. These mechanisms were initially necessary for the evolution of multi-cellular organisms, and became even more important as animals evolved large bodies and long lives. Indeed, the development and architecture of our tissues were evolutionarily constrained by the need to limit cancer. Cancer development within an individual is also an evolutionary process, which in many respects mirrors species evolution. Species evolve by mutation and selection acting on individuals in a population; tumors evolve by mutation and selection acting on cells in a tissue. The processes of mutation and selection are integral to the evolution of cancer at every step of multistage carcinogenesis, from tumor genesis to metastasis. Factors associated with cancer development, such as aging and carcinogens, have been shown to promote cancer evolution by impacting both mutation and selection processes. While there are therapies that can decimate a cancer cell population, unfortunately, cancers can also evolve resistance to these therapies, leading to the resurgence of treatment-refractory disease. Understanding cancer from an evolutionary perspective can allow us to appreciate better why cancers predominantly occur in the elderly, and why other conditions, from radiation exposure to smoking, are associated with increased cancers. Importantly, the application of evolutionary theory to cancer should engender new treatment strategies that could better control this dreaded disease. PMID:23705033

Can Evolutionary Principles Explain Patterns of Family Violence?

ERIC Educational Resources Information Center

Archer, John

2013-01-01

The article's aim is to evaluate the application of the evolutionary principles of kin selection, reproductive value, and resource holding power to the understanding of family violence. The principles are described in relation to specific predictions and the mechanisms underlying these. Predictions are evaluated for physical violence perpetrated…

The genomic landscape of rapid, repeated evolutionary rescue from toxic pollution in wild fish

USDA-ARS?s Scientific Manuscript database

Here we describe evolutionary rescue from intense pollution via multiple modes of selection in killifish populations from 4 urban estuaries of the US eastern seaboard. Comparative transcriptomics and analysis of 384 whole genome sequences show that the functioning of a receptor-based signaling pathw...

Learning the Language of Evolution: Lexical Ambiguity and Word Meaning in Student Explanations

ERIC Educational Resources Information Center

Rector, Meghan A.; Nehm, Ross H.; Pearl, Dennis

2013-01-01

Our study investigates the challenges introduced by students' use of lexically ambiguous language in evolutionary explanations. Specifically, we examined students' meaning of five key terms incorporated into their written evolutionary explanations: "pressure", "select", "adapt", "need", and "must". We utilized a new technological tool known as the…

Teaching about Adaptation: Why Evolutionary History Matters

ERIC Educational Resources Information Center

Kampourakis, Kostas

2013-01-01

Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to…

The Evolution of Personality Variation in Humans and Other Animals

ERIC Educational Resources Information Center

Nettle, Daniel

2006-01-01

A comprehensive evolutionary framework for understanding the maintenance of heritable behavioral variation in humans is yet to be developed. Some evolutionary psychologists have argued that heritable variation will not be found in important, fitness-relevant characteristics because of the winnowing effect of natural selection. This article…

Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns.

PubMed

Grusz, Amanda L; Rothfels, Carl J; Schuettpelz, Eric

2016-08-30

Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which comprises about 10 % of fern diversity and includes the enigmatic vittarioid ferns-an epiphytic, tropical lineage known for dramatically reduced morphologies and radically elongated phylogenetic branch lengths. Using expressed sequence data for 2091 loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes. We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection. We find significant, genome-wide differences in evolutionary rate for vittarioid ferns relative to all other lineages within the Pteridaceae, but we recover few significant correlations between faster/slower vittarioid loci and known functional gene categories. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution. Our results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.

In pursuit of small molecule chemistry for calcium-permeable non-selective TRPC channels – mirage or pot of gold?

PubMed Central

Bon, Robin S; Beech, David J

2013-01-01

The primary purpose of this review is to address the progress towards small molecule modulators of human Transient Receptor Potential Canonical proteins (TRPC1, TRPC3, TRPC4, TRPC5, TRPC6 and TRPC7). These proteins generate channels for calcium and sodium ion entry. They are relevant to many mammalian cell types including acinar gland cells, adipocytes, astrocytes, cardiac myocytes, cochlea hair cells, endothelial cells, epithelial cells, fibroblasts, hepatocytes, keratinocytes, leukocytes, mast cells, mesangial cells, neurones, osteoblasts, osteoclasts, platelets, podocytes, smooth muscle cells, skeletal muscle and tumour cells. There are broad-ranging positive roles of the channels in cell adhesion, migration, proliferation, survival and turning, vascular permeability, hypertrophy, wound-healing, hypo-adiponectinaemia, angiogenesis, neointimal hyperplasia, oedema, thrombosis, muscle endurance, lung hyper-responsiveness, glomerular filtration, gastrointestinal motility, pancreatitis, seizure, innate fear, motor coordination, saliva secretion, mast cell degranulation, cancer cell drug resistance, survival after myocardial infarction, efferocytosis, hypo-matrix metalloproteinase, vasoconstriction and vasodilatation. Known small molecule stimulators of the channels include hyperforin, genistein and rosiglitazone, but there is more progress with inhibitors, some of which have promising potency and selectivity. The inhibitors include 2-aminoethoxydiphenyl borate, 2-aminoquinolines, 2-aminothiazoles, fatty acids, isothiourea derivatives, naphthalene sulfonamides, N-phenylanthranilic acids, phenylethylimidazoles, piperazine/piperidine analogues, polyphenols, pyrazoles and steroids. A few of these agents are starting to be useful as tools for determining the physiological and pathophysiological functions of TRPC channels. We suggest that the pursuit of small molecule modulators for TRPC channels is important but that it requires substantial additional effort and investment before we can reap the rewards of highly potent and selective pharmacological modulators. PMID:23763262

An evolutionary perspective on the systems of adaptive immunity.

PubMed

Müller, Viktor; de Boer, Rob J; Bonhoeffer, Sebastian; Szathmáry, Eörs

2018-02-01

We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of vertebrate immunity, arguing that its origin involved a 'difficult' (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Evolutionary perspectives on wildlife disease: concepts and applications

PubMed Central

Vander Wal, Eric; Garant, Dany; Pelletier, Fanie

2014-01-01

Wildlife disease has the potential to cause significant ecological, socioeconomic, and health impacts. As a result, all tools available need to be employed when host–pathogen dynamics merit conservation or management interventions. Evolutionary principles, such as evolutionary history, phenotypic and genetic variation, and selection, have the potential to unravel many of the complex ecological realities of infectious disease in the wild. Despite this, their application to wildlife disease ecology and management remains in its infancy. In this article, we outline the impetus behind applying evolutionary principles to disease ecology and management issues in the wild. We then introduce articles from this special issue on Evolutionary Perspectives on Wildlife Disease: Concepts and Applications, outlining how each is exemplar of a practical wildlife disease challenge that can be enlightened by applied evolution. Ultimately, we aim to bring new insights to wildlife disease ecology and its management using tools and techniques commonly employed in evolutionary ecology. PMID:25469154

Hidden long evolutionary memory in a model biochemical network

NASA Astrophysics Data System (ADS)

Ali, Md. Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan

2018-04-01

We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a functional core module, random evolutionary drift increases network complexity even in the absence of specific selective pressures. Surprisingly, we uncover a hidden order in sequence space that gives rise to long-term evolutionary memory, implying strong constraints on network evolution due to the topology of accessible sequence space.

Evolutionary response when selection and genetic variation covary across environments.

PubMed

Wood, Corlett W; Brodie, Edmund D

2016-10-01

Although models of evolution usually assume that the strength of selection on a trait and the expression of genetic variation in that trait are independent, whenever the same ecological factor impacts both parameters, a correlation between the two may arise that accelerates trait evolution in some environments and slows it in others. Here, we address the evolutionary consequences and ecological causes of a correlation between selection and expressed genetic variation. Using a simple analytical model, we show that the correlation has a modest effect on the mean evolutionary response and a large effect on its variance, increasing among-population or among-generation variation in the response when positive, and diminishing variation when negative. We performed a literature review to identify the ecological factors that influence selection and expressed genetic variation across traits. We found that some factors - temperature and competition - are unlikely to generate the correlation because they affected one parameter more than the other, and identified others - most notably, environmental novelty - that merit further investigation because little is known about their impact on one of the two parameters. We argue that the correlation between selection and genetic variation deserves attention alongside other factors that promote or constrain evolution in heterogeneous landscapes. © 2016 John Wiley & Sons Ltd/CNRS.

Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model

PubMed Central

Nené, Nuno R.; Dunham, Alistair S.; Illingworth, Christopher J. R.

2018-01-01

A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. The inference of selection may be confounded by the effects of genetic drift in a system, leading to the development of inference procedures to account for these effects. However, recent work has suggested that deterministic models of evolution may be effective in capturing the effects of selection even under complex models of demography, suggesting the more general application of deterministic approaches to inference. Responding to this literature, we here note a case in which a deterministic model of evolution may give highly misleading inferences, resulting from the nondeterministic properties of mutation in a finite population. We propose an alternative approach that acts to correct for this error, and which we denote the delay-deterministic model. Applying our model to a simple evolutionary system, we demonstrate its performance in quantifying the extent of selection acting within that system. We further consider the application of our model to sequence data from an evolutionary experiment. We outline scenarios in which our model may produce improved results for the inference of selection, noting that such situations can be easily identified via the use of a regular deterministic model. PMID:29500183

Brain size evolution in pipefishes and seahorses: the role of feeding ecology, life history and sexual selection.

PubMed

Tsuboi, M; Lim, A C O; Ooi, B L; Yip, M Y; Chong, V C; Ahnesjö, I; Kolm, N

2017-01-01

Brain size varies greatly at all taxonomic levels. Feeding ecology, life history and sexual selection have been proposed as key components in generating contemporary diversity in brain size across vertebrates. Analyses of brain size evolution have, however, been limited to lineages where males predominantly compete for mating and females choose mates. Here, we present the first original data set of brain sizes in pipefishes and seahorses (Syngnathidae) a group in which intense female mating competition occurs in many species. After controlling for the effect of shared ancestry and overall body size, brain size was positively correlated with relative snout length. Moreover, we found that females, on average, had 4.3% heavier brains than males and that polyandrous species demonstrated more pronounced (11.7%) female-biased brain size dimorphism. Our results suggest that adaptations for feeding on mobile prey items and sexual selection in females are important factors in brain size evolution of pipefishes and seahorses. Most importantly, our study supports the idea that sexual selection plays a major role in brain size evolution, regardless of on which sex sexual selection acts stronger. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evolutionary stasis in pollen morphogenesis due to natural selection.

PubMed

Matamoro-Vidal, Alexis; Prieu, Charlotte; Furness, Carol A; Albert, Béatrice; Gouyon, Pierre-Henri

2016-01-01

The contribution of developmental constraints and selective forces to the determination of evolutionary patterns is an important and unsolved question. We test whether the long-term evolutionary stasis observed for pollen morphogenesis (microsporogenesis) in eudicots is due to developmental constraints or to selection on a morphological trait shaped by microsporogenesis: the equatorial aperture pattern. Most eudicots have three equatorial apertures but several taxa have independently lost the equatorial pattern and have microsporogenesis decoupled from aperture pattern determination. If selection on the equatorial pattern limits variation, we expect to see increased variation in microsporogenesis in the nonequatorial clades. Variation of microsporogenesis was studied using phylogenetic comparative analyses in 83 species dispersed throughout eudicots including species with and without equatorial apertures. The species that have lost the equatorial pattern have highly variable microsporogenesis at the intra-individual and inter-specific levels regardless of their pollen morphology, whereas microsporogenesis remains stable in species with the equatorial pattern. The observed burst of variation upon loss of equatorial apertures shows that there are no strong developmental constraints precluding variation in microsporogenesis, and that the stasis is likely to be due principally to selective pressure acting on pollen morphogenesis because of its implication in the determination of the equatorial aperture pattern. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Delta Chromium-53/52 isotopic composition of native and contaminated groundwater, Mojave Desert, USA

USGS Publications Warehouse

Izbicki, John A.; Bullen, Thomas D.; Martin, Peter; Schroth, Brian

2012-01-01

Chromium(VI) concentrations in groundwater sampled from three contaminant plumes in aquifers in the Mojave Desert near Hinkley, Topock and El Mirage, California, USA, were as high as 2600, 5800 and 330 μg/L, respectively. δ53/52Cr compositions from more than 50 samples collected within these plumes ranged from near 0‰ to almost 4‰ near the plume margins. Assuming only reductive fractionation of Cr(VI) to Cr(III) within the plume, apparent fractionation factors for δ53/52Cr isotopes ranged from εapp = 0.3 to 0.4 within the Hinkley and Topock plumes, respectively, and only the El Mirage plume had a fractionation factor similar to the laboratory derived value of ε = 3.5. One possible explanation for the difference between field and laboratory fractionation factors at the Hinkley and Topock sites is localized reductive fractionation of Cr(VI) to Cr(III), with subsequent advective mixing of native and contaminated water near the plume margin. Chromium(VI) concentrations and δ53/52Cr isotopic compositions did not uniquely define the source of Cr near the plume margin, or the extent of reductive fractionation within the plume. However, Cr(VI) and δ53/52Cr data contribute to understanding of the interaction between reductive and mixing processes that occur within and near the margins of Cr contamination plumes. Reductive fractionation of Cr(VI) predominates in plumes having higher εapp, these plumes may be suitable for monitored natural attenuation. In contrast, advective mixing predominates in plumes having lower εapp, the highly dispersed margins of these plumes may be difficult to define and manage.

Directional selection effects on patterns of phenotypic (co)variation in wild populations

PubMed Central

Patton, J. L.; Hubbe, A.; Marroig, G.

2016-01-01

Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus an important gap in evolutionary theory. Here, we documented changes in the phenotypic (co)variation structure in two separate natural populations in each of two chipmunk species (Tamias alpinus and T. speciosus) undergoing directional selection. In populations where selection was strongest (those of T. alpinus), we observed changes, at least for one population, in phenotypic (co)variation that matched theoretical expectations, namely an increase of both phenotypic integration and (co)variance in the direction of selection and a re-alignment of the major axis of variation with the selection gradient. PMID:27881744

Niche construction, sources of selection and trait coevolution.

PubMed

Laland, Kevin; Odling-Smee, John; Endler, John

2017-10-06

Organisms modify and choose components of their local environments. This 'niche construction' can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection directly affecting the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.

The Evolutionary Tempo of Sex Chromosome Degradation in Carica papaya.

PubMed

Wu, Meng; Moore, Richard C

2015-06-01

Genes on non-recombining heterogametic sex chromosomes may degrade over time through the irreversible accumulation of deleterious mutations. In papaya, the non-recombining male-specific region of the Y (MSY) consists of two evolutionary strata corresponding to chromosomal inversions occurring approximately 7.0 and 1.9 MYA. The step-wise recombination suppression between the papaya X and Y allows for a temporal examination of the degeneration progress of the young Y chromosome. Comparative evolutionary analyses of 55 X/Y gene pairs showed that Y-linked genes have more unfavorable substitutions than X-linked genes. However, this asymmetric evolutionary pattern is confined to the oldest stratum, and is only observed when recently evolved pseudogenes are included in the analysis, indicating a slow degeneration tempo of the papaya Y chromosome. Population genetic analyses of coding sequence variation of six Y-linked focal loci in the oldest evolutionary stratum detected an excess of nonsynonymous polymorphism and reduced codon bias relative to autosomal loci. However, this pattern was also observed for corresponding X-linked loci. Both the MSY and its corresponding X-specific region are pericentromeric where recombination has been shown to be greatly reduced. Like the MSY region, overall selective efficacy on the X-specific region may be reduced due to the interference of selective forces between highly linked loci, or the Hill-Robertson effect, that is accentuated in regions of low or suppressed recombination. Thus, a pattern of gene decay on the X-specific region may be explained by relaxed purifying selection and widespread genetic hitchhiking due to its pericentromeric location.

Archaeological data reveal slow rates of evolution during plant domestication.

PubMed

Purugganan, Michael D; Fuller, Dorian Q

2011-01-01

Domestication is an evolutionary process of species divergence in which morphological and physiological changes result from the cultivation/tending of plant or animal species by a mutualistic partner, most prominently humans. Darwin used domestication as an analogy to evolution by natural selection although there is strong debate on whether this process of species evolution by human association is an appropriate model for evolutionary study. There is a presumption that selection under domestication is strong and most models assume rapid evolution of cultivated species. Using archaeological data for 11 species from 60 archaeological sites, we measure rates of evolution in two plant domestication traits--nonshattering and grain/seed size increase. Contrary to previous assumptions, we find the rates of phenotypic evolution during domestication are slow, and significantly lower or comparable to those observed among wild species subjected to natural selection. Our study indicates that the magnitudes of the rates of evolution during the domestication process, including the strength of selection, may be similar to those measured for wild species. This suggests that domestication may be driven by unconscious selection pressures similar to that observed for natural selection, and the study of the domestication process may indeed prove to be a valid model for the study of evolutionary change. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Nonmathematical concepts of selection, evolutionary energy, and levels of evolution.

PubMed

Darlington, P J

1972-05-01

The place of mathematics in hypotheticodeductive processes and in biological research is discussed. (Natural) Selection is defined and described as differential elimination of performed sets at any level. Sets and acting sets are groups of units (themselves sets of smaller units) at any level that may or do interact. A pseudomathematical equation describes directional change (evolution) in sets at any level. Selection is the ram of evolution; it cannot generate, but can only direct, evolutionary energy. The energy of evolution is derived from molecular or chemical levels, is transmitted upwards through the increasingly complex sets of sets that form living systems, and is turned in directions determined by the sum of selective processes, at different levels, which may either supplement or oppose each other. All evolutionary processes conform to the pseudomathematical equation referred to above, use energy as described above, and have a P/OE (ratio of programming to open-endedness) that cannot be measured, but can be related to other P/OE values. Phylogeny and ontogeny are compared as processes af directional change with set selection. Stages in the evolution of multi-cellular individuals are suggested, and are essentially the same as stages in the evolution of some multi-individual insect societies. Thinking is considered as a part of ontogeny involving an irreversible, nonrepetitive process of set selection in the brain.

A comparative analysis of experimental selection on the stickleback pelvis.

PubMed

Miller, S E; Barrueto, M; Schluter, D

2017-06-01

Mechanisms of natural selection can be identified using experimental approaches. However, such experiments often yield nonsignificant effects and imprecise estimates of selection due to low power and small sample sizes. Combining results from multiple experimental studies might produce an aggregate estimate of selection that is more revealing than individual studies. For example, bony pelvic armour varies conspicuously among stickleback populations, and predation by vertebrate and insect predators has been hypothesized to be the main driver of this variation. Yet experimental selection studies testing these hypotheses frequently fail to find a significant effect. We experimentally manipulated length of threespine stickleback (Gasterosteus aculeatus) pelvic spines in a mesocosm experiment to test whether prickly sculpin (Cottus asper), an intraguild predator of stickleback, favours longer spines. The probability of survival was greater for stickleback with unclipped pelvic spines, but this effect was noisy and not significant. We used meta-analysis to combine the results of our mesocosm experiment with previously published experimental studies of selection on pelvic armour. We found evidence that fish predation indeed favours increased pelvic armour, with a moderate effect size. The same approach found little evidence that insect predation favours reduced pelvic armour. The causes of reduced pelvic armour in many stickleback populations remain uncertain. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

A global evolutionary and metabolic analysis of human obesity gene risk variants.

PubMed

Castillo, Joseph J; Hazlett, Zachary S; Orlando, Robert A; Garver, William S

2017-09-05

It is generally accepted that the selection of gene variants during human evolution optimized energy metabolism that now interacts with our obesogenic environment to increase the prevalence of obesity. The purpose of this study was to perform a global evolutionary and metabolic analysis of human obesity gene risk variants (110 human obesity genes with 127 nearest gene risk variants) identified using genome-wide association studies (GWAS) to enhance our knowledge of early and late genotypes. As a result of determining the mean frequency of these obesity gene risk variants in 13 available populations from around the world our results provide evidence for the early selection of ancestral risk variants (defined as selection before migration from Africa) and late selection of derived risk variants (defined as selection after migration from Africa). Our results also provide novel information for association of these obesity genes or encoded proteins with diverse metabolic pathways and other human diseases. The overall results indicate a significant differential evolutionary pattern for the selection of obesity gene ancestral and derived risk variants proposed to optimize energy metabolism in varying global environments and complex association with metabolic pathways and other human diseases. These results are consistent with obesity genes that encode proteins possessing a fundamental role in maintaining energy metabolism and survival during the course of human evolution. Copyright © 2017. Published by Elsevier B.V.

A multivariate analysis of genetic variation in the advertisement call of the gray treefrog, Hyla versicolor.

PubMed

Welch, Allison M; Smith, Michael J; Gerhardt, H Carl

2014-06-01

Genetic variation in sexual displays is crucial for an evolutionary response to sexual selection, but can be eroded by strong selection. Identifying the magnitude and sources of additive genetic variance underlying sexually selected traits is thus an important issue in evolutionary biology. We conducted a quantitative genetics experiment with gray treefrogs (Hyla versicolor) to investigate genetic variances and covariances among features of the male advertisement call. Two energetically expensive traits showed significant genetic variation: call duration, expressed as number of pulses per call, and call rate, represented by its inverse, call period. These two properties also showed significant genetic covariance, consistent with an energetic constraint to call production. Combining the genetic variance-covariance matrix with previous estimates of directional sexual selection imposed by female preferences predicts a limited increase in call duration but no change in call rate despite significant selection on both traits. In addition to constraints imposed by the genetic covariance structure, an evolutionary response to sexual selection may also be limited by high energetic costs of long-duration calls and by preferences that act most strongly against very short-duration calls. Meanwhile, the persistence of these preferences could be explained by costs of mating with males with especially unattractive calls. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Migrate small, sound big: functional constraints on body size promote tracheal elongation in cranes.

PubMed

Jones, M R; Witt, C C

2014-06-01

Organismal traits often represent the outcome of opposing selection pressures. Although social or sexual selection can cause the evolution of traits that constrain function or survival (e.g. ornamental feathers), it is unclear how the strength and direction of selection respond to ecological shifts that increase the severity of the constraint. For example, reduced body size might evolve by natural selection to enhance flight performance in migratory birds, but social or sexual selection favouring large body size may provide a countervailing force. Tracheal elongation is a potential outcome of these opposing pressures because it allows birds to convey an auditory signal of exaggerated body size. We predicted that the evolution of migration in cranes has coincided with a reduction in body size and a concomitant intensification of social or sexual selection for apparent large body size via tracheal elongation. We used a phylogenetic comparative approach to examine the relationships among migration distance, body mass and trachea length in cranes. As predicted, we found that migration distance correlated negatively with body size and positively with proportional trachea length. This result was consistent with our hypothesis that evolutionary reductions in body size led to intensified selection for trachea length. The most likely ultimate causes of intensified positive selection on trachea length are the direct benefits of conveying a large body size in intraspecific contests for mates and territories. We conclude that the strength of social or sexual selection on crane body size is linked to the degree of functional constraint. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

A quantum of natural selection

NASA Astrophysics Data System (ADS)

Lloyd, Seth

2009-03-01

The modern evolutionary synthesis, which marries Darwin's theory of natural selection with Mendel's genetics, was developed around the same time as quantum mechanics. Is there any connection between the two?

The genetic basis of traits regulating sperm competition and polyandry: can selection favour the evolution of good- and sexy-sperm?

PubMed

Evans, Jonathan P; Simmons, Leigh W

2008-09-01

The good-sperm and sexy-sperm (GS-SS) hypotheses predict that female multiple mating (polyandry) can fuel sexual selection for heritable male traits that promote success in sperm competition. A major prediction generated by these models, therefore, is that polyandry will benefit females indirectly via their sons' enhanced fertilization success. Furthermore, like classic 'good genes' and 'sexy son' models for the evolution of female preferences, GS-SS processes predict a genetic correlation between genes for female mating frequency (analogous to the female preference) and those for traits influencing fertilization success (the sexually selected traits). We examine the premise for these predictions by exploring the genetic basis of traits thought to influence fertilization success and female mating frequency. We also highlight recent debates that stress the possible genetic constraints to evolution of traits influencing fertilization success via GS-SS processes, including sex-linked inheritance, nonadditive effects, interacting parental genotypes, and trade-offs between integrated ejaculate components. Despite these possible constraints, the available data suggest that male traits involved in sperm competition typically exhibit substantial additive genetic variance and rapid evolutionary responses to selection. Nevertheless, the limited data on the genetic variation in female mating frequency implicate strong genetic maternal effects, including X-linkage, which is inconsistent with GS-SS processes. Although the relative paucity of studies on the genetic basis of polyandry does not allow us to draw firm conclusions about the evolutionary origins of this trait, the emerging pattern of sex linkage in genes for polyandry is more consistent with an evolutionary history of antagonistic selection over mating frequency. We advocate further development of GS-SS theory to take account of the complex evolutionary dynamics imposed by sexual conflict over mating frequency.

Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks.

PubMed

Billiard, Sylvain; Ferrière, Régis; Méléard, Sylvie; Tran, Viet Chi

2015-11-01

How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.

Foundational errors in the Neutral and Nearly-Neutral theories of evolution in relation to the Synthetic Theory: is a new evolutionary paradigm necessary?

PubMed

Valenzuela, Carlos Y

2013-01-01

The Neutral Theory of Evolution (NTE) proposes mutation and random genetic drift as the most important evolutionary factors. The most conspicuous feature of evolution is the genomic stability during paleontological eras and lack of variation among taxa; 98% or more of nucleotide sites are monomorphic within a species. NTE explains this homology by random fixation of neutral bases and negative selection (purifying selection) that does not contribute either to evolution or polymorphisms. Purifying selection is insufficient to account for this evolutionary feature and the Nearly-Neutral Theory of Evolution (N-NTE) included negative selection with coefficients as low as mutation rate. These NTE and N-NTE propositions are thermodynamically (tendency to random distributions, second law), biotically (recurrent mutation), logically and mathematically (resilient equilibria instead of fixation by drift) untenable. Recurrent forward and backward mutation and random fluctuations of base frequencies alone in a site make life organization and fixations impossible. Drift is not a directional evolutionary factor, but a directional tendency of matter-energy processes (second law) which threatens the biotic organization. Drift cannot drive evolution. In a site, the mutation rates among bases and selection coefficients determine the resilient equilibrium frequency of bases that genetic drift cannot change. The expected neutral random interaction among nucleotides is zero; however, huge interactions and periodicities were found between bases of dinucleotides separated by 1, 2... and more than 1,000 sites. Every base is co-adapted with the whole genome. Neutralists found that neutral evolution is independent of population size (N); thus neutral evolution should be independent of drift, because drift effect is dependent upon N. Also, chromosome size and shape as well as protein size are far from random.

Why Darwin would have loved evolutionary game theory

PubMed Central

2016-01-01

Humans have marvelled at the fit of form and function, the way organisms' traits seem remarkably suited to their lifestyles and ecologies. While natural selection provides the scientific basis for the fit of form and function, Darwin found certain adaptations vexing or particularly intriguing: sex ratios, sexual selection and altruism. The logic behind these adaptations resides in frequency-dependent selection where the value of a given heritable phenotype (i.e. strategy) to an individual depends upon the strategies of others. Game theory is a branch of mathematics that is uniquely suited to solving such puzzles. While game theoretic thinking enters into Darwin's arguments and those of evolutionists through much of the twentieth century, the tools of evolutionary game theory were not available to Darwin or most evolutionists until the 1970s, and its full scope has only unfolded in the last three decades. As a consequence, game theory is applied and appreciated rather spottily. Game theory not only applies to matrix games and social games, it also applies to speciation, macroevolution and perhaps even to cancer. I assert that life and natural selection are a game, and that game theory is the appropriate logic for framing and understanding adaptations. Its scope can include behaviours within species, state-dependent strategies (such as male, female and so much more), speciation and coevolution, and expands beyond microevolution to macroevolution. Game theory clarifies aspects of ecological and evolutionary stability in ways useful to understanding eco-evolutionary dynamics, niche construction and ecosystem engineering. In short, I would like to think that Darwin would have found game theory uniquely useful for his theory of natural selection. Let us see why this is so. PMID:27605503

Why Darwin would have loved evolutionary game theory.

PubMed

Brown, Joel S

2016-09-14

Humans have marvelled at the fit of form and function, the way organisms' traits seem remarkably suited to their lifestyles and ecologies. While natural selection provides the scientific basis for the fit of form and function, Darwin found certain adaptations vexing or particularly intriguing: sex ratios, sexual selection and altruism. The logic behind these adaptations resides in frequency-dependent selection where the value of a given heritable phenotype (i.e. strategy) to an individual depends upon the strategies of others. Game theory is a branch of mathematics that is uniquely suited to solving such puzzles. While game theoretic thinking enters into Darwin's arguments and those of evolutionists through much of the twentieth century, the tools of evolutionary game theory were not available to Darwin or most evolutionists until the 1970s, and its full scope has only unfolded in the last three decades. As a consequence, game theory is applied and appreciated rather spottily. Game theory not only applies to matrix games and social games, it also applies to speciation, macroevolution and perhaps even to cancer. I assert that life and natural selection are a game, and that game theory is the appropriate logic for framing and understanding adaptations. Its scope can include behaviours within species, state-dependent strategies (such as male, female and so much more), speciation and coevolution, and expands beyond microevolution to macroevolution. Game theory clarifies aspects of ecological and evolutionary stability in ways useful to understanding eco-evolutionary dynamics, niche construction and ecosystem engineering. In short, I would like to think that Darwin would have found game theory uniquely useful for his theory of natural selection. Let us see why this is so. © 2016 The Author(s).

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

PubMed Central

Wang, Jing; Street, Nathaniel R.; Scofield, Douglas G.; Ingvarsson, Pär K.

2016-01-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. PMID:26721855

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

PubMed

Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

2016-03-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. Copyright © 2016 by the Genetics Society of America.

Nonequivalence of updating rules in evolutionary games under high mutation rates.

PubMed

Kaiping, G A; Jacobs, G S; Cox, S J; Sluckin, T J

2014-10-01

Moran processes are often used to model selection in evolutionary simulations. The updating rule in Moran processes is a birth-death process, i. e., selection according to fitness of an individual to give birth, followed by the death of a random individual. For well-mixed populations with only two strategies this updating rule is known to be equivalent to selecting unfit individuals for death and then selecting randomly for procreation (biased death-birth process). It is, however, known that this equivalence does not hold when considering structured populations. Here we study whether changing the updating rule can also have an effect in well-mixed populations in the presence of more than two strategies and high mutation rates. We find, using three models from different areas of evolutionary simulation, that the choice of updating rule can change model results. We show, e. g., that going from the birth-death process to the death-birth process can change a public goods game with punishment from containing mostly defectors to having a majority of cooperative strategies. From the examples given we derive guidelines indicating when the choice of the updating rule can be expected to have an impact on the results of the model.

The genomic landscape of rapid repeated evolutionary ...

EPA Pesticide Factsheets

Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediatinggenes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversityhas likely been a crucial substrate for selective sweeps to propel rapid adaptation. This manuscript describes genomic evaluations that contribute to our understanding of the ecological and evolutionary risks associated with chronic contaminant exposures to wildlife populations. Here, we assessed genetic patterns associated with long-term response to an important class of highly toxic environmental pollutants. Specifically, chemical-specific tolerance has rapidly and repeatedly evolved in an estuarine fish species resident to estuaries of the Atlantic U.S. coast. We used laboratory studies to ch

The accumulation of reproductive isolation in early stages of divergence supports a role for sexual selection.

PubMed

Martin, M D; Mendelson, T C

2016-04-01

Models of speciation by sexual selection propose that male-female coevolution leads to the rapid evolution of behavioural reproductive isolation. Here, we compare the strength of behavioural isolation to ecological isolation, gametic incompatibility and hybrid inviability in a group of dichromatic stream fishes. In addition, we examine whether any of these individual barriers, or a combined measure of total isolation, is predicted by body shape differences, male colour differences, environmental differences or genetic distance. Behavioural isolation reaches the highest values of any barrier and is significantly greater than ecological isolation. No individual reproductive barrier is associated with any of the predictor variables. However, marginally significant relationships between male colour and body shape differences with ecological and behavioural isolation are discussed. Differences in male colour and body shape predict total reproductive isolation between species; hierarchical partitioning of these two variables' effects suggests a stronger role for male colour differences. Together, these results suggest an important role for divergent sexual selection in darter speciation but raise new questions about the mechanisms of sexual selection at play and the role of male nuptial ornaments. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Public goods games in populations with fluctuating size.

PubMed

McAvoy, Alex; Fraiman, Nicolas; Hauert, Christoph; Wakeley, John; Nowak, Martin A

2018-05-01

Many mathematical frameworks of evolutionary game dynamics assume that the total population size is constant and that selection affects only the relative frequency of strategies. Here, we consider evolutionary game dynamics in an extended Wright-Fisher process with variable population size. In such a scenario, it is possible that the entire population becomes extinct. Survival of the population may depend on which strategy prevails in the game dynamics. Studying cooperative dilemmas, it is a natural feature of such a model that cooperators enable survival, while defectors drive extinction. Although defectors are favored for any mixed population, random drift could lead to their elimination and the resulting pure-cooperator population could survive. On the other hand, if the defectors remain, then the population will quickly go extinct because the frequency of cooperators steadily declines and defectors alone cannot survive. In a mutation-selection model, we find that (i) a steady supply of cooperators can enable long-term population survival, provided selection is sufficiently strong, and (ii) selection can increase the abundance of cooperators but reduce their relative frequency. Thus, evolutionary game dynamics in populations with variable size generate a multifaceted notion of what constitutes a trait's long-term success. Copyright © 2018 Elsevier Inc. All rights reserved.

Nonequivalence of updating rules in evolutionary games under high mutation rates

NASA Astrophysics Data System (ADS)

Kaiping, G. A.; Jacobs, G. S.; Cox, S. J.; Sluckin, T. J.

2014-10-01

Moran processes are often used to model selection in evolutionary simulations. The updating rule in Moran processes is a birth-death process, i. e., selection according to fitness of an individual to give birth, followed by the death of a random individual. For well-mixed populations with only two strategies this updating rule is known to be equivalent to selecting unfit individuals for death and then selecting randomly for procreation (biased death-birth process). It is, however, known that this equivalence does not hold when considering structured populations. Here we study whether changing the updating rule can also have an effect in well-mixed populations in the presence of more than two strategies and high mutation rates. We find, using three models from different areas of evolutionary simulation, that the choice of updating rule can change model results. We show, e. g., that going from the birth-death process to the death-birth process can change a public goods game with punishment from containing mostly defectors to having a majority of cooperative strategies. From the examples given we derive guidelines indicating when the choice of the updating rule can be expected to have an impact on the results of the model.

Neutral evolution in a biological population as diffusion in phenotype space: reproduction with local mutation but without selection.

PubMed

Lawson, Daniel John; Jensen, Henrik Jeldtoft

2007-03-02

The process of "evolutionary diffusion," i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.

An evolutionary medicine approach to understanding factors that contribute to chronic obstructive pulmonary disease.

PubMed

Aoshiba, Kazutetsu; Tsuji, Takao; Itoh, Masayuki; Yamaguchi, Kazuhiro; Nakamura, Hiroyuki

2015-01-01

Although many studies have been published on the causes and mechanisms of chronic obstructive pulmonary disease (COPD), the reason for the existence of COPD and the reasons why COPD develops in humans have hardly been studied. Evolutionary medical approaches are required to explain not only the proximate factors, such as the causes and mechanisms of a disease, but the ultimate (evolutionary) factors as well, such as why the disease is present and why the disease develops in humans. According to the concepts of evolutionary medicine, disease susceptibility is acquired as a result of natural selection during the evolutionary process of traits linked to the genes involved in disease susceptibility. In this paper, we discuss the following six reasons why COPD develops in humans based on current evolutionary medical theories: (1) evolutionary constraints; (2) mismatch between environmental changes and evolution; (3) co-evolution with pathogenic microorganisms; (4) life history trade-off; (5) defenses and their costs, and (6) reproductive success at the expense of health. Our perspective pursues evolutionary answers to the fundamental question, 'Why are humans susceptible to this common disease, COPD, despite their long evolutionary history?' We believe that the perspectives offered by evolutionary medicine are essential for researchers to better understand the significance of their work.

Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis

PubMed Central

Chu, Xin-Yi; Zhou, Xiong-Hui; Cui, Ze-Jia; Zhang, Hong-Yu

2017-01-01

The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information. PMID:28708071

Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis.

PubMed

Chu, Xin-Yi; Jiang, Ling-Han; Zhou, Xiong-Hui; Cui, Ze-Jia; Zhang, Hong-Yu

2017-07-14

The cancer atavistic theory suggests that carcinogenesis is a reverse evolution process. It is thus of great interest to explore the evolutionary origins of cancer driver genes and the relevant mechanisms underlying the carcinogenesis. Moreover, the evolutionary features of cancer driver genes could be helpful in selecting cancer biomarkers from high-throughput data. In this study, through analyzing the cancer endogenous molecular networks, we revealed that the subnetwork originating from eukaryota could control the unlimited proliferation of cancer cells, and the subnetwork originating from eumetazoa could recapitulate the other hallmarks of cancer. In addition, investigations based on multiple datasets revealed that cancer driver genes were enriched in genes originating from eukaryota, opisthokonta, and eumetazoa. These results have important implications for enhancing the robustness of cancer prognosis models through selecting the gene signatures by the gene age information.

An evolutionary approach to financial history.

PubMed

Ferguson, N

2009-01-01

Financial history is not conventionally thought of in evolutionary terms, but it should be. Traditional ways of thinking about finance, dating back to Hilferding, emphasize the importance of concentration and economies of scale. But these approaches overlook the rich "biodiversity" that characterizes the financial world. They also overlook the role of natural selection. To be sure, natural selection in the financial world is not exactly analogous to the processes first described by Darwin and elaborated on by modern biologists. There is conscious adaptation as well as random mutation. Moreover, there is something resembling "intelligent design" in finance, whereby regulators and legislators act in a quasidivine capacity, putting dinosaurs on life support. The danger is that such interventions in the natural processes of the market may ultimately distort the evolutionary process, by getting in the way of Schumpeter's "creative destruction."

Darwin's Difficulties and Students' Struggles with Trait Loss: Cognitive-Historical Parallelisms in Evolutionary Explanation

ERIC Educational Resources Information Center

Ha, Minsu; Nehm, Ross H.

2014-01-01

Although historical changes in scientific ideas sometimes display striking similarities with students' conceptual progressions, some scholars have cautioned that such similarities lack meaningful commonalities. In the history of evolution, while Darwin and his contemporaries often used natural selection to explain evolutionary trait gain or…

Evolutionary Psychology: A Natural Selection for Music Education?

ERIC Educational Resources Information Center

Graham, Rodger

2006-01-01

In this viewpoint it is suggested that recent research and authorship in the evolutionary psychology (EP) of music can provide musicians and educators with an enriched understanding of the adaptive role of music in human life. Within a climate of continual educational reform in which music is often marginalised from other mainstream curricular…

Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization

USDA-ARS?s Scientific Manuscript database

Meishan is a famous Chinese indigenous pig breed known for its extremely high fecundity. To explore if Meishan has unique evolutionary process and genome characteristics differing from other pig breeds, we systematically analyzed its genetic divergence, and demographic history by large-scale reseque...

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention.

PubMed

Johnston, Iain G; Williams, Ben P

2016-02-24

Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species. Copyright © 2016 Elsevier Inc. All rights reserved.

Evolutionary dynamics on graphs

NASA Astrophysics Data System (ADS)

Lieberman, Erez; Hauert, Christoph; Nowak, Martin A.

2005-01-01

Evolutionary dynamics have been traditionally studied in the context of homogeneous or spatially extended populations. Here we generalize population structure by arranging individuals on a graph. Each vertex represents an individual. The weighted edges denote reproductive rates which govern how often individuals place offspring into adjacent vertices. The homogeneous population, described by the Moran process, is the special case of a fully connected graph with evenly weighted edges. Spatial structures are described by graphs where vertices are connected with their nearest neighbours. We also explore evolution on random and scale-free networks. We determine the fixation probability of mutants, and characterize those graphs for which fixation behaviour is identical to that of a homogeneous population. Furthermore, some graphs act as suppressors and others as amplifiers of selection. It is even possible to find graphs that guarantee the fixation of any advantageous mutant. We also study frequency-dependent selection and show that the outcome of evolutionary games can depend entirely on the structure of the underlying graph. Evolutionary graph theory has many fascinating applications ranging from ecology to multi-cellular organization and economics.

Can Ebola virus evolve to be less virulent in humans?

PubMed

Sofonea, M T; Aldakak, L; Boullosa, L F V V; Alizon, S

2018-03-01

Understanding Ebola virus (EBOV) virulence evolution not only is timely but also raises specific questions because it causes one of the most virulent human infections and it is capable of transmission after the death of its host. Using a compartmental epidemiological model that captures three transmission routes (by regular contact, via dead bodies and by sexual contact), we infer the evolutionary dynamics of case fatality ratio on the scale of an outbreak and in the long term. Our major finding is that the virus's specific life cycle imposes selection for high levels of virulence and that this pattern is robust to parameter variations in biological ranges. In addition to shedding a new light on the ultimate causes of EBOV's high virulence, these results generate testable predictions and contribute to informing public health policies. In particular, burial management stands out as the most appropriate intervention since it decreases the R0 of the epidemics, while imposing selection for less virulent strains. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Evolutionary game theory using agent-based methods.

PubMed

Adami, Christoph; Schossau, Jory; Hintze, Arend

2016-12-01

Evolutionary game theory is a successful mathematical framework geared towards understanding the selective pressures that affect the evolution of the strategies of agents engaged in interactions with potential conflicts. While a mathematical treatment of the costs and benefits of decisions can predict the optimal strategy in simple settings, more realistic settings such as finite populations, non-vanishing mutations rates, stochastic decisions, communication between agents, and spatial interactions, require agent-based methods where each agent is modeled as an individual, carries its own genes that determine its decisions, and where the evolutionary outcome can only be ascertained by evolving the population of agents forward in time. While highlighting standard mathematical results, we compare those to agent-based methods that can go beyond the limitations of equations and simulate the complexity of heterogeneous populations and an ever-changing set of interactors. We conclude that agent-based methods can predict evolutionary outcomes where purely mathematical treatments cannot tread (for example in the weak selection-strong mutation limit), but that mathematics is crucial to validate the computational simulations. Copyright © 2016 Elsevier B.V. All rights reserved.

Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm

PubMed Central

Jin, Xiaoli; Ren, Jing; Nevo, Eviatar; Yin, Xuegui; Sun, Dongfa; Peng, Junhua

2017-01-01

NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1) uneven constitution of Clusters of Orthologous Groups (COGs) and contrasting birth/death rates among subfamilies, and (2) two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses. PMID:28713414

Connecting theory and data to understand recombination rate evolution.

PubMed

Dapper, Amy L; Payseur, Bret A

2017-12-19

Meiotic recombination is necessary for successful gametogenesis in most sexually reproducing organisms and is a fundamental genomic parameter, influencing the efficacy of selection and the fate of new mutations. The molecular and evolutionary functions of recombination should impose strong selective constraints on the range of recombination rates. Yet, variation in recombination rate is observed on a variety of genomic and evolutionary scales. In the past decade, empirical studies have described variation in recombination rate within genomes, between individuals, between sexes, between populations and between species. At the same time, theoretical work has provided an increasingly detailed picture of the evolutionary advantages to recombination. Perhaps surprisingly, the causes of natural variation in recombination rate remain poorly understood. We argue that empirical and theoretical approaches to understand the evolution of recombination have proceeded largely independently of each other. Most models that address the evolution of recombination rate were created to explain the evolutionary advantage of recombination rather than quantitative differences in rate among individuals. Conversely, most empirical studies aim to describe variation in recombination rate, rather than to test evolutionary hypotheses. In this Perspective, we argue that efforts to integrate the rich bodies of empirical and theoretical work on recombination rate are crucial to moving this field forward. We provide new directions for the development of theory and the production of data that will jointly close this gap.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'. © 2017 The Author(s).

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts

PubMed Central

Troupin, Cécile; Dacheux, Laurent; Tanguy, Marion; Sabeta, Claude; Blanc, Hervé; Bouchier, Christiane; Vignuzzi, Marco; Holmes, Edward C.; Bourhy, Hervé

2016-01-01

The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics. PMID:27977811

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

PubMed Central

Mohammed, Jaaved; Flynt, Alex S.; Siepel, Adam; Lai, Eric C.

2013-01-01

The molecular evolutionary signatures of miRNAs inform our understanding of their emergence, biogenesis, and function. The known signatures of miRNA evolution have derived mostly from the analysis of deeply conserved, canonical loci. In this study, we examine the impact of age, biogenesis pathway, and genomic arrangement on the evolutionary properties of Drosophila miRNAs. Crucial to the accuracy of our results was our curation of high-quality miRNA alignments, which included nearly 150 corrections to ortholog calls and nucleotide sequences of the global 12-way Drosophilid alignments currently available. Using these data, we studied primary sequence conservation, normalized free-energy values, and types of structure-preserving substitutions. We expand upon common miRNA evolutionary patterns that reflect fundamental features of miRNAs that are under functional selection. We observe that melanogaster-subgroup-specific miRNAs, although recently emerged and rapidly evolving, nonetheless exhibit evolutionary signatures that are similar to well-conserved miRNAs and distinct from other structured noncoding RNAs and bulk conserved non-miRNA hairpins. This provides evidence that even young miRNAs may be selected for regulatory activities. More strikingly, we observe that mirtrons and clustered miRNAs both exhibit distinct evolutionary properties relative to solo, well-conserved miRNAs, even after controlling for sequence depth. These studies highlight the previously unappreciated impact of biogenesis strategy and genomic location on the evolutionary dynamics of miRNAs, and affirm that miRNAs do not evolve as a unitary class. PMID:23882112

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

PubMed

Troupin, Cécile; Dacheux, Laurent; Tanguy, Marion; Sabeta, Claude; Blanc, Hervé; Bouchier, Christiane; Vignuzzi, Marco; Duchene, Sebastián; Holmes, Edward C; Bourhy, Hervé

2016-12-01

The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.

Can evolutionary principles explain patterns of family violence?

PubMed

Archer, John

2013-03-01

The article's aim is to evaluate the application of the evolutionary principles of kin selection, reproductive value, and resource holding power to the understanding of family violence. The principles are described in relation to specific predictions and the mechanisms underlying these. Predictions are evaluated for physical violence perpetrated by (a) parents to unrelated children, (b) parents to genetic offspring, and (c) offspring to parents and between (d) siblings and (e) sexual partners. Precise figures for risks have been calculated where possible. The major conclusions are that most of the evidence is consistent with evolutionary predictions derived from kin selection and reproductive value: There were (a) higher rates of violence to stepchildren, (b) a decline in violence with the age of offspring, and (c) an increase in violence with parental age, while (d) violence between siblings was generally at a low level and concerned resource disputes. The issue of distinguishing evolutionary from alternative explanations is addressed throughout and is problematic for predictions derived from reproductive value. The main evolutionary explanation for male partner violence, mate guarding as a result of paternity uncertainty, cannot explain Western studies where sex differences in control and violence between partners were absent, although other aspects of male partner violence are consistent with it, and it may explain sex differences in traditional cultures. Recurrent problems in evaluating the evidence were to control for possible confounds and thus to distinguish evolutionary from alternative explanations. Suggestions are outlined to address this and other issues arising from the review. © 2013 American Psychological Association

How Darwinian is cultural evolution?

PubMed Central

Claidière, Nicolas; Scott-Phillips, Thomas C.; Sperber, Dan

2014-01-01

Darwin-inspired population thinking suggests approaching culture as a population of items of different types, whose relative frequencies may change over time. Three nested subtypes of populational models can be distinguished: evolutionary, selectional and replicative. Substantial progress has been made in the study of cultural evolution by modelling it within the selectional frame. This progress has involved idealizing away from phenomena that may be critical to an adequate understanding of culture and cultural evolution, particularly the constructive aspect of the mechanisms of cultural transmission. Taking these aspects into account, we describe cultural evolution in terms of cultural attraction, which is populational and evolutionary, but only selectional under certain circumstances. As such, in order to model cultural evolution, we must not simply adjust existing replicative or selectional models but we should rather generalize them, so that, just as replicator-based selection is one form that Darwinian selection can take, selection itself is one of several different forms that attraction can take. We present an elementary formalization of the idea of cultural attraction. PMID:24686939

Signatures of Sex-Antagonistic Selection on Recombining Sex Chromosomes

PubMed Central

Kirkpatrick, Mark; Guerrero, Rafael F.

2014-01-01

Sex-antagonistic (SA) selection has major evolutionary consequences: it can drive genomic change, constrain adaptation, and maintain genetic variation for fitness. The recombining (or pseudoautosomal) regions of sex chromosomes are a promising setting in which to study SA selection because they tend to accumulate SA polymorphisms and because recombination allows us to deploy the tools of molecular evolution to locate targets of SA selection and quantify evolutionary forces. Here we use coalescent models to characterize the patterns of polymorphism expected within and divergence between recombining X and Y (or Z and W) sex chromosomes. SA selection generates peaks of divergence between X and Y that can extend substantial distances away from the targets of selection. Linkage disequilibrium between neutral sites is also inflated. We show how the pattern of divergence is altered when the SA polymorphism or the sex-determining region was recently established. We use data from the flowering plant Silene latifolia to illustrate how the strength of SA selection might be quantified using molecular data from recombining sex chromosomes. PMID:24578352

How Darwinian is cultural evolution?

PubMed

Claidière, Nicolas; Scott-Phillips, Thomas C; Sperber, Dan

2014-05-19

Darwin-inspired population thinking suggests approaching culture as a population of items of different types, whose relative frequencies may change over time. Three nested subtypes of populational models can be distinguished: evolutionary, selectional and replicative. Substantial progress has been made in the study of cultural evolution by modelling it within the selectional frame. This progress has involved idealizing away from phenomena that may be critical to an adequate understanding of culture and cultural evolution, particularly the constructive aspect of the mechanisms of cultural transmission. Taking these aspects into account, we describe cultural evolution in terms of cultural attraction, which is populational and evolutionary, but only selectional under certain circumstances. As such, in order to model cultural evolution, we must not simply adjust existing replicative or selectional models but we should rather generalize them, so that, just as replicator-based selection is one form that Darwinian selection can take, selection itself is one of several different forms that attraction can take. We present an elementary formalization of the idea of cultural attraction.

Long-legged bees make adaptive leaps: linking adaptation to coevolution in a plant-pollinator network.

PubMed

Pauw, Anton; Kahnt, Belinda; Kuhlmann, Michael; Michez, Denis; Montgomery, Graham A; Murray, Elizabeth; Danforth, Bryan N

2017-09-13

Adaptation is evolution in response to natural selection. Hence, an adaptation is expected to originate simultaneously with the acquisition of a particular selective environment. Here we test whether long legs evolve in oil-collecting Rediviva bees when they come under selection by long-spurred, oil-secreting flowers. To quantify the selective environment, we drew a large network of the interactions between Rediviva species and oil-secreting plant species. The selective environment of each bee species was summarized as the average spur length of the interacting plant species weighted by interaction frequency. Using phylogenetically independent contrasts, we calculated divergence in selective environment and evolutionary divergence in leg length between sister species (and sister clades) of Rediviva We found that change in the selective environment explained 80% of evolutionary change in leg length, with change in body size contributing an additional 6% of uniquely explained variance. The result is one of four proposed steps in testing for plant-pollinator coevolution. © 2017 The Author(s).

Quantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug Targets.

PubMed

Brooks, Lauren E; Ul-Hasan, Sabah; Chan, Benjamin K; Sistrom, Mark J

2018-01-01

Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have been identified as the leading global cause of multidrug-resistant bacterial infections, and overexpression of multidrug efflux (MEX) transport systems has been identified as one of the most critical mechanisms facilitating the evolution of multidrug resistance in ESKAPE pathogens. Despite efforts to develop efflux pump inhibitors to combat antibiotic resistance, the need persists to identify additional targets for future investigations. We evaluated evolutionary pressures on 110 MEX-encoding genes from all annotated ESKAPE organism genomes. We identify several MEX genes under stabilizing selection-representing targets which can facilitate broad-spectrum treatments with evolutionary constraints limiting the potential emergence of escape mutants. We also examine MEX systems being evaluated as drug targets, demonstrating that divergent selection may underlie some of the problems encountered in the development of effective treatments-specifically in relation to the NorA system in S. aureus. This study provides a comprehensive evolutionary context to efflux in the ESKAPE pathogens, which will provide critical context to the evaluation of efflux systems as antibiotic targets. IMPORTANCE Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogen group represents the leading cause of these infections, and upregulation of efflux pump expression is a significant mechanism of resistance in these pathogens. This has resulted in substantial interest in the development of efflux pump inhibitors to combat antibiotic-resistant infections; however, no widespread treatments have been developed to date. Our study evaluates an often-underappreciated aspect of resistance-the impact of evolutionary selection. We evaluate selection on all annotated efflux genes in all sequenced ESKAPE pathogens, providing critical context for and insight into current and future development of efflux-targeting treatments for resistant bacterial infections.

Evolutionary responses by native species to major anthropogenic changes to their ecosystems: Pacific salmon in the Columbia River hydropower system.

PubMed

Waples, Robin S; Zabel, Richard W; Scheuerell, Mark D; Sanderson, Beth L

2008-01-01

The human footprint is now large in all the Earth's ecosystems, and construction of large dams in major river basins is among the anthropogenic changes that have had the most profound ecological consequences, particularly for migratory fishes. In the Columbia River basin of the western USA, considerable effort has been directed toward evaluating demographic effects of dams, yet little attention has been paid to evolutionary responses of migratory salmon to altered selective regimes. Here we make a first attempt to address this information gap. Transformation of the free-flowing Columbia River into a series of slack-water reservoirs has relaxed selection for adults capable of migrating long distances upstream against strong flows; conditions now favour fish capable of migrating through lakes and finding and navigating fish ladders. Juveniles must now be capable of surviving passage through multiple dams or collection and transportation around the dams. River flow patterns deliver some groups of juvenile salmon to the estuary later than is optimal for ocean survival, but countervailing selective pressures might constrain an evolutionary response toward earlier migration timing. Dams have increased the cost of migration, which reduces energy available for sexual selection and favours a nonmigratory life history. Reservoirs are a benign environment for many non-native species that are competitors with or predators on salmon, and evolutionary responses are likely (but undocumented). More research is needed to tease apart the relative importance of evolutionary vs. plastic responses of salmon to these environmental changes; this research is logistically challenging for species with life histories like Pacific salmon, but results should substantially improve our understanding of key processes. If the Columbia River is ever returned to a quasinatural, free-flowing state, remaining populations might face a Darwinian debt (and temporarily reduced fitness) as they struggle to re-evolve historical adaptations.

Selection and constraints on offspring size-number trade-offs in sand lizards (Lacerta agilis).

PubMed

Ljungström, G; Stjernstedt, M; Wapstra, E; Olsson, M

2016-05-01

The trade-off between offspring size and number is a central component of life-history theory, postulating that larger investment into offspring size inevitably decreases offspring number. This trade-off is generally discussed in terms of genetic, physiological or morphological constraints; however, as among-individual differences can mask individual trade-offs, the underlying mechanisms may be difficult to reveal. In this study, we use multivariate analyses to investigate whether there is a trade-off between offspring size and number in a population of sand lizards by separating among- and within-individual patterns using a 15-year data set collected in the wild. We also explore the ecological and evolutionary causes and consequences of this trade-off by investigating how a female's resource (condition)- vs. age-related size (snout-vent length) influences her investment into offspring size vs. number (OSN), whether these traits are heritable and under selection and whether the OSN trade-off has a genetic component. We found a negative correlation between offspring size and number within individual females and physical constraints (size of body cavity) appear to limit the number of eggs that a female can produce. This suggests that the OSN trade-off occurs due to resource constraints as a female continues to grow throughout life and, thus, produces larger clutches. In contrast to the assumptions of classic OSN theory, we did not detect selection on offspring size; however, there was directional selection for larger clutch sizes. The repeatabilities of both offspring size and number were low and we did not detect any additive genetic variance in either trait. This could be due to strong selection (past or current) on these life-history traits, or to insufficient statistical power to detect significant additive genetic effects. Overall, the findings of this study are an important illustration of how analyses of within-individual patterns can reveal trade-offs and their underlying causes, with potential evolutionary and ecological consequences that are otherwise hidden by among-individual variation. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Genetic architecture and balancing selection: the life and death of differentiated variants.

PubMed

Llaurens, Violaine; Whibley, Annabel; Joron, Mathieu

2017-05-01

Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems. © 2017 John Wiley & Sons Ltd.

Quantifying Selective Pressures Driving Bacterial Evolution Using Lineage Analysis

NASA Astrophysics Data System (ADS)

Lambert, Guillaume; Kussell, Edo

2015-01-01

Organisms use a variety of strategies to adapt to their environments and maximize long-term growth potential, but quantitative characterization of the benefits conferred by the use of such strategies, as well as their impact on the whole population's rate of growth, remains challenging. Here, we use a path-integral framework that describes how selection acts on lineages—i.e., the life histories of individuals and their ancestors—to demonstrate that lineage-based measurements can be used to quantify the selective pressures acting on a population. We apply this analysis to Escherichia coli bacteria exposed to cyclical treatments of carbenicillin, an antibiotic that interferes with cell-wall synthesis and affects cells in an age-dependent manner. While the extensive characterization of the life history of thousands of cells is necessary to accurately extract the age-dependent selective pressures caused by carbenicillin, the same measurement can be recapitulated using lineage-based statistics of a single surviving cell. Population-wide evolutionary pressures can be extracted from the properties of the surviving lineages within a population, providing an alternative and efficient procedure to quantify the evolutionary forces acting on a population. Importantly, this approach is not limited to age-dependent selection, and the framework can be generalized to detect signatures of other trait-specific selection using lineage-based measurements. Our results establish a powerful way to study the evolutionary dynamics of life under selection and may be broadly useful in elucidating selective pressures driving the emergence of antibiotic resistance and the evolution of survival strategies in biological systems.

Quantifying selective pressures driving bacterial evolution using lineage analysis

PubMed Central

Lambert, Guillaume; Kussell, Edo

2015-01-01

Organisms use a variety of strategies to adapt to their environments and maximize long-term growth potential, but quantitative characterization of the benefits conferred by the use of such strategies, as well as their impact on the whole population’s rate of growth, remains challenging. Here, we use a path-integral framework that describes how selection acts on lineages –i.e. the life-histories of individuals and their ancestors– to demonstrate that lineage-based measurements can be used to quantify the selective pressures acting on a population. We apply this analysis to E. coli bacteria exposed to cyclical treatments of carbenicillin, an antibiotic that interferes with cell-wall synthesis and affects cells in an age-dependent manner. While the extensive characterization of the life-history of thousands of cells is necessary to accurately extract the age-dependent selective pressures caused by carbenicillin, the same measurement can be recapitulated using lineage-based statistics of a single surviving cell. Population-wide evolutionary pressures can be extracted from the properties of the surviving lineages within a population, providing an alternative and efficient procedure to quantify the evolutionary forces acting on a population. Importantly, this approach is not limited to age-dependent selection, and the framework can be generalized to detect signatures of other trait-specific selection using lineage-based measurements. Our results establish a powerful way to study the evolutionary dynamics of life under selection, and may be broadly useful in elucidating selective pressures driving the emergence of antibiotic resistance and the evolution of survival strategies in biological systems. PMID:26213639

Quantifying selection in evolving populations using time-resolved genetic data

NASA Astrophysics Data System (ADS)

Illingworth, Christopher J. R.; Mustonen, Ville

2013-01-01

Methods which uncover the molecular basis of the adaptive evolution of a population address some important biological questions. For example, the problem of identifying genetic variants which underlie drug resistance, a question of importance for the treatment of pathogens, and of cancer, can be understood as a matter of inferring selection. One difficulty in the inference of variants under positive selection is the potential complexity of the underlying evolutionary dynamics, which may involve an interplay between several contributing processes, including mutation, recombination and genetic drift. A source of progress may be found in modern sequencing technologies, which confer an increasing ability to gather information about evolving populations, granting a window into these complex processes. One particularly interesting development is the ability to follow evolution as it happens, by whole-genome sequencing of an evolving population at multiple time points. We here discuss how to use time-resolved sequence data to draw inferences about the evolutionary dynamics of a population under study. We begin by reviewing our earlier analysis of a yeast selection experiment, in which we used a deterministic evolutionary framework to identify alleles under selection for heat tolerance, and to quantify the selection acting upon them. Considering further the use of advanced intercross lines to measure selection, we here extend this framework to cover scenarios of simultaneous recombination and selection, and of two driver alleles with multiple linked neutral, or passenger, alleles, where the driver pair evolves under an epistatic fitness landscape. We conclude by discussing the limitations of the approach presented and outlining future challenges for such methodologies.

Protein interface classification by evolutionary analysis

PubMed Central

2012-01-01

Background Distinguishing biologically relevant interfaces from lattice contacts in protein crystals is a fundamental problem in structural biology. Despite efforts towards the computational prediction of interface character, many issues are still unresolved. Results We present here a protein-protein interface classifier that relies on evolutionary data to detect the biological character of interfaces. The classifier uses a simple geometric measure, number of core residues, and two evolutionary indicators based on the sequence entropy of homolog sequences. Both aim at detecting differential selection pressure between interface core and rim or rest of surface. The core residues, defined as fully buried residues (>95% burial), appear to be fundamental determinants of biological interfaces: their number is in itself a powerful discriminator of interface character and together with the evolutionary measures it is able to clearly distinguish evolved biological contacts from crystal ones. We demonstrate that this definition of core residues leads to distinctively better results than earlier definitions from the literature. The stringent selection and quality filtering of structural and sequence data was key to the success of the method. Most importantly we demonstrate that a more conservative selection of homolog sequences - with relatively high sequence identities to the query - is able to produce a clearer signal than previous attempts. Conclusions An evolutionary approach like the one presented here is key to the advancement of the field, which so far was missing an effective method exploiting the evolutionary character of protein interfaces. Its coverage and performance will only improve over time thanks to the incessant growth of sequence databases. Currently our method reaches an accuracy of 89% in classifying interfaces of the Ponstingl 2003 datasets and it lends itself to a variety of useful applications in structural biology and bioinformatics. We made the corresponding software implementation available to the community as an easy-to-use graphical web interface at http://www.eppic-web.org. PMID:23259833

Positive evolutionary selection of an HD motif on Alzheimer precursor protein orthologues suggests a functional role.

PubMed

Miklós, István; Zádori, Zoltán

2012-02-01

HD amino acid duplex has been found in the active center of many different enzymes. The dyad plays remarkably different roles in their catalytic processes that usually involve metal coordination. An HD motif is positioned directly on the amyloid beta fragment (Aβ) and on the carboxy-terminal region of the extracellular domain (CAED) of the human amyloid precursor protein (APP) and a taxonomically well defined group of APP orthologues (APPOs). In human Aβ HD is part of a presumed, RGD-like integrin-binding motif RHD; however, neither RHD nor RXD demonstrates reasonable conservation in APPOs. The sequences of CAEDs and the position of the HD are not particularly conserved either, yet we show with a novel statistical method using evolutionary modeling that the presence of HD on CAEDs cannot be the result of neutral evolutionary forces (p<0.0001). The motif is positively selected along the evolutionary process in the majority of APPOs, despite the fact that HD motif is underrepresented in the proteomes of all species of the animal kingdom. Position migration can be explained by high probability occurrence of multiple copies of HD on intermediate sequences, from which only one is kept by selective evolutionary forces, in a similar way as in the case of the "transcription binding site turnover." CAED of all APP orthologues and homologues are predicted to bind metal ions including Amyloid-like protein 1 (APLP1) and Amyloid-like protein 2 (APLP2). Our results suggest that HDs on the CAEDs are most probably key components of metal-binding domains, which facilitate and/or regulate inter- or intra-molecular interactions in a metal ion-dependent or metal ion concentration-dependent manner. The involvement of naturally occurring mutations of HD (Tottori (D7N) and English (H6R) mutations) in early onset Alzheimer's disease gives additional support to our finding that HD has an evolutionary preserved function on APPOs.

Positive Evolutionary Selection of an HD Motif on Alzheimer Precursor Protein Orthologues Suggests a Functional Role

PubMed Central

Miklós, István; Zádori, Zoltán

2012-01-01

HD amino acid duplex has been found in the active center of many different enzymes. The dyad plays remarkably different roles in their catalytic processes that usually involve metal coordination. An HD motif is positioned directly on the amyloid beta fragment (Aβ) and on the carboxy-terminal region of the extracellular domain (CAED) of the human amyloid precursor protein (APP) and a taxonomically well defined group of APP orthologues (APPOs). In human Aβ HD is part of a presumed, RGD-like integrin-binding motif RHD; however, neither RHD nor RXD demonstrates reasonable conservation in APPOs. The sequences of CAEDs and the position of the HD are not particularly conserved either, yet we show with a novel statistical method using evolutionary modeling that the presence of HD on CAEDs cannot be the result of neutral evolutionary forces (p<0.0001). The motif is positively selected along the evolutionary process in the majority of APPOs, despite the fact that HD motif is underrepresented in the proteomes of all species of the animal kingdom. Position migration can be explained by high probability occurrence of multiple copies of HD on intermediate sequences, from which only one is kept by selective evolutionary forces, in a similar way as in the case of the “transcription binding site turnover.” CAED of all APP orthologues and homologues are predicted to bind metal ions including Amyloid-like protein 1 (APLP1) and Amyloid-like protein 2 (APLP2). Our results suggest that HDs on the CAEDs are most probably key components of metal-binding domains, which facilitate and/or regulate inter- or intra-molecular interactions in a metal ion-dependent or metal ion concentration-dependent manner. The involvement of naturally occurring mutations of HD (Tottori (D7N) and English (H6R) mutations) in early onset Alzheimer's disease gives additional support to our finding that HD has an evolutionary preserved function on APPOs. PMID:22319430

Buried treasure: evolutionary perspectives on microbial iron piracy

PubMed Central

Barber, Matthew F.; Elde, Nels C.

2015-01-01

Host-pathogen interactions provide valuable systems for the study of evolutionary genetics and natural selection. The sequestration of essential iron has emerged as a critical innate defense system termed nutritional immunity, leading pathogens to evolve mechanisms of `iron piracy' to scavenge this metal from host proteins. This battle for iron carries numerous consequences not only for host-pathogen evolution, but also microbial community interactions. Here we highlight recent and potential future areas of investigation on the evolutionary implications of microbial iron piracy in relation to molecular arms races, host range, competition, and virulence. Applying evolutionary genetic approaches to the study of microbial iron acquisition could also provide new inroads for understanding and combating infectious disease. PMID:26431675

Misrepresentations of evolutionary psychology in sex and gender textbooks.

PubMed

Winegard, Benjamin M; Winegard, Bo M; Deaner, Robert O

2014-05-20

Evolutionary psychology has provoked controversy, especially when applied to human sex differences. We hypothesize that this is partly due to misunderstandings of evolutionary psychology that are perpetuated by undergraduate sex and gender textbooks. As an initial test of this hypothesis, we develop a catalog of eight types of errors and document their occurrence in 15 widely used sex and gender textbooks. Consistent with our hypothesis, of the 12 textbooks that discussed evolutionary psychology, all contained at least one error, and the median number of errors was five. The most common types of errors were "Straw Man," "Biological Determinism," and "Species Selection." We conclude by suggesting improvements to undergraduate sex and gender textbooks.

Evolution of proliferation and the angiogenic switch in tumors with high clonal diversity.

PubMed

Bickel, Scott T; Juliano, Joseph D; Nagy, John D

2014-01-01

Natural selection among tumor cell clones is thought to produce hallmark properties of malignancy. Efforts to understand evolution of one such hallmark--the angiogenic switch--has suggested that selection for angiogenesis can "run away" and generate a hypertumor, a form of evolutionary suicide by extreme vascular hypo- or hyperplasia. This phenomenon is predicted by models of tumor angiogenesis studied with the techniques of adaptive dynamics. These techniques also predict that selection drives tumor proliferative potential towards an evolutionarily stable strategy (ESS) that is also convergence-stable. However, adaptive dynamics are predicated on two key assumptions: (i) no more than two distinct clones or evolutionary strategies can exist in the tumor at any given time; and (ii) mutations cause small phenotypic changes. Here we show, using a stochastic simulation, that relaxation of these assumptions has no effect on the predictions of adaptive dynamics in this case. In particular, selection drives proliferative potential towards, and angiogenic potential away from, their respective ESSs. However, these simulations also show that tumor behavior is highly contingent on mutational history, particularly for angiogenesis. Individual tumors frequently grow to lethal size before the evolutionary endpoint is approached. In fact, most tumor dynamics are predicted to be in the evolutionarily transient regime throughout their natural history, so that clinically, the ESS is often largely irrelevant. In addition, we show that clonal diversity as measured by the Shannon Information Index correlates with the speed of approach to the evolutionary endpoint. This observation dovetails with results showing that clonal diversity in Barrett's esophagus predicts progression to malignancy.

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems.

PubMed

Sauterey, Boris; Ward, Ben A; Follows, Michael J; Bowler, Chris; Claessen, David

2015-01-01

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that "Everything is everywhere, but the environment selects", we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean.

Evolutionary graph theory: breaking the symmetry between interaction and replacement

PubMed Central

Ohtsuki, Hisashi; Pacheco, Jorge M.; Nowak, Martin A.

2008-01-01

We study evolutionary dynamics in a population whose structure is given by two graphs: the interaction graph determines who plays with whom in an evolutionary game; the replacement graph specifies the geometry of evolutionary competition and updating. First, we calculate the fixation probabilities of frequency dependent selection between two strategies or phenotypes. We consider three different update mechanisms: birth-death, death-birth and imitation. Then, as a particular example, we explore the evolution of cooperation. Suppose the interaction graph is a regular graph of degree h, the replacement graph is a regular graph of degree g and the overlap between the two graphs is a regular graph of degree l. We show that cooperation is favored by natural selection if b/c > hg/l. Here, b and c denote the benefit and cost of the altruistic act. This result holds for death-birth updating, weak selection and large population size. Note that the optimum population structure for cooperators is given by maximum overlap between the interaction and the replacement graph (g = h = l), which means that the two graphs are identical. We also prove that a modified replicator equation can describe how the expected values of the frequencies of an arbitrary number of strategies change on replacement and interaction graphs: the two graphs induce a transformation of the payoff matrix. PMID:17350049

What affects the predictability of evolutionary constraints using a G-matrix? The relative effects of modular pleiotropy and mutational correlation.

PubMed

Chebib, Jobran; Guillaume, Frédéric

2017-10-01

Phenotypic traits do not always respond to selection independently from each other and often show correlated responses to selection. The structure of a genotype-phenotype map (GP map) determines trait covariation, which involves variation in the degree and strength of the pleiotropic effects of the underlying genes. It is still unclear, and debated, how much of that structure can be deduced from variational properties of quantitative traits that are inferred from their genetic (co) variance matrix (G-matrix). Here we aim to clarify how the extent of pleiotropy and the correlation among the pleiotropic effects of mutations differentially affect the structure of a G-matrix and our ability to detect genetic constraints from its eigen decomposition. We show that the eigenvectors of a G-matrix can be predictive of evolutionary constraints when they map to underlying pleiotropic modules with correlated mutational effects. Without mutational correlation, evolutionary constraints caused by the fitness costs associated with increased pleiotropy are harder to infer from evolutionary metrics based on a G-matrix's geometric properties because uncorrelated pleiotropic effects do not affect traits' genetic correlations. Correlational selection induces much weaker modular partitioning of traits' genetic correlations in absence then in presence of underlying modular pleiotropy. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Evolution of increased competitiveness in cows trades off with reduced milk yield, fertility and more masculine morphology.

PubMed

Sartori, Cristina; Mazza, Serena; Guzzo, Nadia; Mantovani, Roberto

2015-08-01

In some species females compete for food, foraging territories, mating, and nesting sites. Competing females can exhibit morphological, physiological, and behavioral adaptations typical of males, which are commonly considered as secondary sexual traits. Competition and the development of traits increasing competitiveness require much energy and may exert adverse effects on fecundity and survival. From an evolutionary perspective, positive selection for increased competitiveness would then result in evolution of reduced values for traits related to fitness such as fecundity and survival. There is recent evidence for such evolutionary trade-offs involving male competition, but no study has considered competing females so far. Using data from competitions for dominance in cows (Bos taurus), we found negative genetic correlations between traits providing success in competition, that is, fighting ability and fitness traits related to milk production and with fertility (the inverse of parity-conception interval). Fighting ability also showed low but positive genetic correlations with "masculine" morphological traits, and negative correlations with "feminine" traits. A genetic change in traits over time has occurred due to selection on competitiveness, corresponding to an evolutionary process of "masculinization" counteracting the official selection for milk yield. Similar evolutionary trade-off between success in competition and fitness components may be present in various species experiencing female competition. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Genomic evidence of gene duplication and adaptive evolution of Toll like receptors (TLR2 and TLR4) in reptiles.

PubMed

Shang, Shuai; Zhong, Huaming; Wu, Xiaoyang; Wei, Qinguo; Zhang, Huanxin; Chen, Jun; Chen, Yao; Tang, Xuexi; Zhang, Honghai

2018-04-01

Toll-like receptors (TLRs) encoded by the TLR multigene family play an important role in initial pathogen recognition in vertebrates. Among the TLRs, TLR2 and TLR4 may be of particular importance to reptiles. In order to study the evolutionary patterns and structural characteristics of TLRs, we explored the available genomes of several representative members of reptiles. 25 TLR2 genes and 19 TLR4 genes from reptiles were obtained in this study. Phylogenetic results showed that the TLR2 gene duplication occurred in several species. Evolutionary analysis by at least two methods identified 30 and 13 common positively selected codons in TLR2 and TLR4, respectively. Most positively selected sites of TLR2 and TLR4 were located in the Leucine-rich repeat (LRRs). Branch model analysis showed that TLR2 genes were under different evolutionary forces in reptiles, while the TLR4 genes showed no significant selection pressure. The different evolutionary adaptation of TLR2 and TLR4 among the reptiles might be due to their different function in recognizing bacteria. Overall, we explored the structure and evolution of TLR2 and TLR4 genes in reptiles for the first time. Our study revealed valuable information regarding TLR2 and TLR4 in reptiles, and provided novel insights into the conservation concern of natural populations. Copyright © 2017 Elsevier B.V. All rights reserved.

Atmospheric refraction: a history.

PubMed

Lehn, Waldemar H; van der Werf, Siebren

2005-09-20

We trace the history of atmospheric refraction from the ancient Greeks up to the time of Kepler. The concept that the atmosphere could refract light entered Western science in the second century B.C. Ptolemy, 300 years later, produced the first clearly defined atmospheric model, containing air of uniform density up to a sharp upper transition to the ether, at which the refraction occurred. Alhazen and Witelo transmitted his knowledge to medieval Europe. The first accurate measurements were made by Tycho Brahe in the 16th century. Finally, Kepler, who was aware of unusually strong refractions, used the Ptolemaic model to explain the first documented and recognized mirage (the Novaya Zemlya effect).

Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals

PubMed Central

2011-01-01

Background Matrix extracellular phosphoglycoprotein (MEPE) belongs to a family of small integrin-binding ligand N-linked glycoproteins (SIBLINGs) that play a key role in skeleton development, particularly in mineralization, phosphate regulation and osteogenesis. MEPE associated disorders cause various physiological effects, such as loss of bone mass, tumors and disruption of renal function (hypophosphatemia). The study of this developmental gene from an evolutionary perspective could provide valuable insights on the adaptive diversification of morphological phenotypes in vertebrates. Results Here we studied the adaptive evolution of the MEPE gene in 26 Eutherian mammals and three birds. The comparative genomic analyses revealed a high degree of evolutionary conservation of some coding and non-coding regions of the MEPE gene across mammals indicating a possible regulatory or functional role likely related with mineralization and/or phosphate regulation. However, the majority of the coding region had a fast evolutionary rate, particularly within the largest exon (1467 bp). Rodentia and Scandentia had distinct substitution rates with an increased accumulation of both synonymous and non-synonymous mutations compared with other mammalian lineages. Characteristics of the gene (e.g. biochemical, evolutionary rate, and intronic conservation) differed greatly among lineages of the eight mammalian orders. We identified 20 sites with significant positive selection signatures (codon and protein level) outside the main regulatory motifs (dentonin and ASARM) suggestive of an adaptive role. Conversely, we find three sites under selection in the signal peptide and one in the ASARM motif that were supported by at least one selection model. The MEPE protein tends to accumulate amino acids promoting disorder and potential phosphorylation targets. Conclusion MEPE shows a high number of selection signatures, revealing the crucial role of positive selection in the evolution of this SIBLING member. The selection signatures were found mainly outside the functional motifs, reinforcing the idea that other regions outside the dentonin and the ASARM might be crucial for the function of the protein and future studies should be undertaken to understand its importance. PMID:22103247

Parental effects and the evolution of phenotypic memory.

PubMed

Kuijper, B; Johnstone, R A

2016-02-01

Despite growing evidence for nongenetic inheritance, the ecological conditions that favour the evolution of heritable parental or grandparental effects remain poorly understood. Here, we systematically explore the evolution of parental effects in a patch-structured population with locally changing environments. When selection favours the production of a mix of offspring types, this mix differs according to the parental phenotype, implying that parental effects are favoured over selection for bet-hedging in which the mixture of offspring phenotypes produced does not depend on the parental phenotype. Positive parental effects (generating a positive correlation between parental and offspring phenotype) are favoured in relatively stable habitats and when different types of local environment are roughly equally abundant, and can give rise to long-term parental inheritance of phenotypes. By contrast, unstable habitats can favour negative parental effects (generating a negative correlation between parental and offspring phenotype), and under these circumstances, even slight asymmetries in the abundance of local environmental states select for marked asymmetries in transmission fidelity. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

The sources of adaptive variation

PubMed Central

2017-01-01

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed. PMID:28566483

The sources of adaptive variation.

PubMed

Charlesworth, Deborah; Barton, Nicholas H; Charlesworth, Brian

2017-05-31

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed. © 2017 The Author(s).

A standard deviation selection in evolutionary algorithm for grouper fish feed formulation

NASA Astrophysics Data System (ADS)

Cai-Juan, Soong; Ramli, Razamin; Rahman, Rosshairy Abdul

2016-10-01

Malaysia is one of the major producer countries for fishery production due to its location in the equatorial environment. Grouper fish is one of the potential markets in contributing to the income of the country due to its desirable taste, high demand and high price. However, the demand of grouper fish is still insufficient from the wild catch. Therefore, there is a need to farm grouper fish to cater to the market demand. In order to farm grouper fish, there is a need to have prior knowledge of the proper nutrients needed because there is no exact data available. Therefore, in this study, primary data and secondary data are collected even though there is a limitation of related papers and 30 samples are investigated by using standard deviation selection in Evolutionary algorithm. Thus, this study would unlock frontiers for an extensive research in respect of grouper fish feed formulation. Results shown that the fitness of standard deviation selection in evolutionary algorithm is applicable. The feasible and low fitness, quick solution can be obtained. These fitness can be further predicted to minimize cost in farming grouper fish.

Viruses and mobile elements as drivers of evolutionary transitions

PubMed Central

2016-01-01

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431520

Viruses and mobile elements as drivers of evolutionary transitions.

PubMed

Koonin, Eugene V

2016-08-19

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of 'public goods'. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host-parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions.This article is part of the themed issue 'The major synthetic evolutionary transitions'. © 2016 The Authors.

Characterizing behavioural ‘characters’: an evolutionary framework

PubMed Central

Araya-Ajoy, Yimen G.; Dingemanse, Niels J.

2014-01-01

Biologists often study phenotypic evolution assuming that phenotypes consist of a set of quasi-independent units that have been shaped by selection to accomplish a particular function. In the evolutionary literature, such quasi-independent functional units are called ‘evolutionary characters’, and a framework based on evolutionary principles has been developed to characterize them. This framework mainly focuses on ‘fixed’ characters, i.e. those that vary exclusively between individuals. In this paper, we introduce multi-level variation and thereby expand the framework to labile characters, focusing on behaviour as a worked example. We first propose a concept of ‘behavioural characters’ based on the original evolutionary character concept. We then detail how integration of variation between individuals (cf. ‘personality’) and within individuals (cf. ‘individual plasticity’) into the framework gives rise to a whole suite of novel testable predictions about the evolutionary character concept. We further propose a corresponding statistical methodology to test whether observed behaviours should be considered expressions of a hypothesized evolutionary character. We illustrate the application of our framework by characterizing the behavioural character ‘aggressiveness’ in wild great tits, Parus major. PMID:24335984

Sex-specific selection under environmental stress in seed beetles.

PubMed

Martinossi-Allibert, I; Arnqvist, G; Berger, D

2017-01-01

Sexual selection can increase rates of adaptation by imposing strong selection in males, thereby allowing efficient purging of the mutation load on population fitness at a low demographic cost. Indeed, sexual selection tends to be male-biased throughout the animal kingdom, but little empirical work has explored the ecological sensitivity of this sex difference. In this study, we generated theoretical predictions of sex-specific strengths of selection, environmental sensitivities and genotype-by-environment interactions and tested them in seed beetles by manipulating either larval host plant or rearing temperature. Using fourteen isofemale lines, we measured sex-specific reductions in fitness components, genotype-by-environment interactions and the strength of selection (variance in fitness) in the juvenile and adult stage. As predicted, variance in fitness increased with stress, was consistently greater in males than females for adult reproductive success (implying strong sexual selection), but was similar in the sexes in terms of juvenile survival across all levels of stress. Although genetic variance in fitness increased in magnitude under severe stress, heritability decreased and particularly so in males. Moreover, genotype-by-environment interactions for fitness were common but specific to the type of stress, sex and life stage, suggesting that new environments may change the relative alignment and strength of selection in males and females. Our study thus exemplifies how environmental stress can influence the relative forces of natural and sexual selection, as well as concomitant changes in genetic variance in fitness, which are predicted to have consequences for rates of adaptation in sexual populations. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Boltzmann, Darwin and Directionality theory

NASA Astrophysics Data System (ADS)

Demetrius, Lloyd A.

2013-09-01

Boltzmann’s statistical thermodynamics is a mathematical theory which relates the macroscopic properties of aggregates of interacting molecules with the laws of their interaction. The theory is based on the concept thermodynamic entropy, a statistical measure of the extent to which energy is spread throughout macroscopic matter. Macroscopic evolution of material aggregates is quantitatively explained in terms of the principle: Thermodynamic entropy increases as the composition of the aggregate changes under molecular collision. Darwin’s theory of evolution is a qualitative theory of the origin of species and the adaptation of populations to their environment. A central concept in the theory is fitness, a qualitative measure of the capacity of an organism to contribute to the ancestry of future generations. Macroscopic evolution of populations of living organisms can be qualitatively explained in terms of a neo-Darwinian principle: Fitness increases as the composition of the population changes under variation and natural selection. Directionality theory is a quantitative model of the Darwinian argument of evolution by variation and selection. This mathematical theory is based on the concept evolutionary entropy, a statistical measure which describes the rate at which an organism appropriates energy from the environment and reinvests this energy into survivorship and reproduction. According to directionality theory, microevolutionary dynamics, that is evolution by mutation and natural selection, can be quantitatively explained in terms of a directionality principle: Evolutionary entropy increases when the resources are diverse and of constant abundance; but decreases when the resource is singular and of variable abundance. This report reviews the analytical and empirical support for directionality theory, and invokes the microevolutionary dynamics of variation and selection to delineate the principles which govern macroevolutionary dynamics of speciation and extinction. We also elucidate the relation between thermodynamic entropy, which pertains to the extent of energy spreading and sharing within inanimate matter, and evolutionary entropy, which refers to the rate of energy appropriation from the environment and allocation within living systems. We show that the entropic principle of thermodynamics is the limit as R→0, M→∞, (where R denote the resource production rate, and M denote population size) of the entropic principle of evolution. We exploit this relation between the thermodynamic and evolutionary tenets to propose a physico-chemical model of the transition from inanimate matter which is under thermodynamic selection, to living systems which are subject to evolutionary selection. Life history variation and the evolution of senescence The evolutionary dynamics of speciation and extinction Evolutionary trends in body size. The origin of sporadic forms of cancer and neurological diseases, and the evolution of cooperation are important recent applications of directionality theory. These applications, which draw from the medical sciences and sociobiology, appeal to methods which lie outside the formalism described in this report. A companion review, Demetrius and Gundlach (submitted for publication), gives an account of these applications.An important aspect of this report pertains to the connection between statistical mechanics and evolutionary theory and its implications towards understanding the processes which underlie the emergence of living systems from inanimate matter-a problem which has recently attracted considerable attention, Morowitz (1992), Eigen (1992), Dyson (2000), Pross (2012).The connection between the two disciplines can be addressed by appealing to certain extremal principles which are considered the mainstay of the respective theories.The extremal principle in statistical mechanics can be stated as follows:

Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis.

PubMed

He, Peng; Huang, Sheng; Xiao, Guanghui; Zhang, Yuzhou; Yu, Jianing

2016-12-01

RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance. In this paper, we investigated 82 protein-coding genes in the chloroplast genome of G. biloba and identified 255 editing sites, which is the highest number of RNA editing events reported in a gymnosperm. All of the editing sites were C-to-U conversions, which mainly occurred in the second codon position, biased towards to the U_A context, and caused an increase in hydrophobic amino acids. RNA editing could change the secondary structures of 82 proteins, and create or eliminate a transmembrane region in five proteins as determined in silico. Finally, the evolutionary tendencies of RNA editing in different gene groups were estimated using the nonsynonymous-synonymous substitution rate selection mode. The G. biloba chloroplast genome possesses the highest number of RNA editing events reported so far in a seed plant. Most of the RNA editing sites can restore amino acid conservation, increase hydrophobicity, and even influence protein structures. Similar purifying selections constitute the dominant evolutionary force at the editing sites of essential genes, such as the psa, some psb and pet groups, and a positive selection occurred in the editing sites of nonessential genes, such as most ndh and a few psb genes.

High evolutionary potential of marine zooplankton

PubMed Central

Peijnenburg, Katja T C A; Goetze, Erica

2013-01-01

Abstract Open ocean zooplankton often have been viewed as slowly evolving species that have limited capacity to respond adaptively to changing ocean conditions. Hence, attention has focused on the ecological responses of zooplankton to current global change, including range shifts and changing phenology. Here, we argue that zooplankton also are well poised for evolutionary responses to global change. We present theoretical arguments that suggest plankton species may respond rapidly to selection on mildly beneficial mutations due to exceptionally large population size, and consider the circumstantial evidence that supports our inference that selection may be particularly important for these species. We also review all primary population genetic studies of open ocean zooplankton and show that genetic isolation can be achieved at the scale of gyre systems in open ocean habitats (100s to 1000s of km). Furthermore, population genetic structure often varies across planktonic taxa, and appears to be linked to the particular ecological requirements of the organism. In combination, these characteristics should facilitate adaptive evolution to distinct oceanographic habitats in the plankton. We conclude that marine zooplankton may be capable of rapid evolutionary as well as ecological responses to changing ocean conditions, and discuss the implications of this view. We further suggest two priority areas for future research to test our hypothesis of high evolutionary potential in open ocean zooplankton, which will require (1) assessing how pervasive selection is in driving population divergence and (2) rigorously quantifying the spatial and temporal scales of population differentiation in the open ocean. Recent attention has focused on the ecological responses of open ocean zooplankton to current global change, including range shifts and changing phenology. Here, we argue that marine zooplankton also are well poised for evolutionary responses to global change. PMID:24567838

75 FR 66803 - Advisory Committee On Reactor Safeguards (ACRS); Meeting of the ACRS Subcommittee on Evolutionary...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-29

... NUCLEAR REGULATORY COMMISSION Advisory Committee On Reactor Safeguards (ACRS); Meeting of the ACRS Subcommittee on Evolutionary Power Reactor (EPR); Notice of Meeting The ACRS Subcommittee on EPR will hold a..., November 30, 2010--8:30 a.m. Until 2 p.m. The Subcommittee will review Selected Chapters of the US EPR...

The evolution of reciprocity in sizable human groups.

PubMed

Rothschild, Casey G

2009-04-21

The scale and complexity of human cooperation is an important and unresolved evolutionary puzzle. This article uses the finitely repeated n person Prisoners' Dilemma game to illustrate how sapience can greatly enhance group-selection effects and lead to the evolutionary stability of cooperation in large groups. This affords a simple and direct explanation of the human "exception".

Is Exercise Really Medicine? An Evolutionary Perspective.

PubMed

Lieberman, Daniel E

2015-01-01

An evolutionary perspective helps evaluate the extent to which exercise is medicine and to explain the exercise paradox: why people tend to avoid exercise despite its benefits. Many lines of evidence indicate that humans evolved to be adapted for regular, moderate amounts of endurance physical activity into late age. However, because energy from food was limited, humans also were selected to avoid unnecessary exertion, and most anatomical and physiological systems evolved to require stimuli from physical activity to adjust capacity to demand. Consequently, selection never operated to cope with the long-term effects of chronic inactivity. However, because all adaptations involve trade-offs, there is no evolutionary-determined dose or type of physical activity that will optimize health. Furthermore, because humans evolved to be active for play or necessity, efforts to promote exercise will require altering environments in ways that nudge or even compel people to be active and to make exercise fun.

Integrating instance selection, instance weighting, and feature weighting for nearest neighbor classifiers by coevolutionary algorithms.

PubMed

Derrac, Joaquín; Triguero, Isaac; Garcia, Salvador; Herrera, Francisco

2012-10-01

Cooperative coevolution is a successful trend of evolutionary computation which allows us to define partitions of the domain of a given problem, or to integrate several related techniques into one, by the use of evolutionary algorithms. It is possible to apply it to the development of advanced classification methods, which integrate several machine learning techniques into a single proposal. A novel approach integrating instance selection, instance weighting, and feature weighting into the framework of a coevolutionary model is presented in this paper. We compare it with a wide range of evolutionary and nonevolutionary related methods, in order to show the benefits of the employment of coevolution to apply the techniques considered simultaneously. The results obtained, contrasted through nonparametric statistical tests, show that our proposal outperforms other methods in the comparison, thus becoming a suitable tool in the task of enhancing the nearest neighbor classifier.

Evolutionary biology: variation isn't always sexy.

PubMed

Safran, Rebecca J; Hauber, Mark E

2007-05-15

A recent study has found that differences in a male trait, considered a textbook example of sexual selection, are in fact due to naturally selected variation in the aerodynamic optimum for each individual.

Applying Evolutionary Anthropology

PubMed Central

Gibson, Mhairi A; Lawson, David W

2015-01-01

Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561

Applying evolutionary anthropology.

PubMed

Gibson, Mhairi A; Lawson, David W

2015-01-01

Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. © 2015 Wiley Periodicals, Inc.

Mate-sampling costs and sexy sons.

PubMed

Kokko, H; Booksmythe, I; Jennions, M D

2015-01-01

Costly female mating preferences for purely Fisherian male traits (i.e. sexual ornaments that are genetically uncorrelated with inherent viability) are not expected to persist at equilibrium. The indirect benefit of producing 'sexy sons' (Fisher process) disappears: in some models, the male trait becomes fixed; in others, a range of male trait values persist, but a larger trait confers no net fitness advantage because it lowers survival. Insufficient indirect selection to counter the direct cost of producing fewer offspring means that preferences are lost. The only well-cited exception assumes biased mutation on male traits. The above findings generally assume constant direct selection against female preferences (i.e. fixed costs). We show that if mate-sampling costs are instead derived based on an explicit account of how females acquire mates, an initially costly mating preference can coevolve with a male trait so that both persist in the presence or absence of biased mutation. Our models predict that empirically detecting selection at equilibrium will be difficult, even if selection was responsible for the location of the current equilibrium. In general, it appears useful to integrate mate sampling theory with models of genetic consequences of mating preferences: being explicit about the process by which individuals select mates can alter equilibria. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model.

PubMed

Nené, Nuno R; Dunham, Alistair S; Illingworth, Christopher J R

2018-05-01

A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. The inference of selection may be confounded by the effects of genetic drift in a system, leading to the development of inference procedures to account for these effects. However, recent work has suggested that deterministic models of evolution may be effective in capturing the effects of selection even under complex models of demography, suggesting the more general application of deterministic approaches to inference. Responding to this literature, we here note a case in which a deterministic model of evolution may give highly misleading inferences, resulting from the nondeterministic properties of mutation in a finite population. We propose an alternative approach that acts to correct for this error, and which we denote the delay-deterministic model. Applying our model to a simple evolutionary system, we demonstrate its performance in quantifying the extent of selection acting within that system. We further consider the application of our model to sequence data from an evolutionary experiment. We outline scenarios in which our model may produce improved results for the inference of selection, noting that such situations can be easily identified via the use of a regular deterministic model. Copyright © 2018 Nené et al.

Neutral Evolution in a Biological Population as Diffusion in Phenotype Space: Reproduction with Local Mutation but without Selection

NASA Astrophysics Data System (ADS)

Lawson, Daniel John; Jensen, Henrik Jeldtoft

2007-03-01

The process of “evolutionary diffusion,” i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.

Evolution of high-level resistance during low-level antibiotic exposure.

PubMed

Wistrand-Yuen, Erik; Knopp, Michael; Hjort, Karin; Koskiniemi, Sanna; Berg, Otto G; Andersson, Dan I

2018-04-23

It has become increasingly clear that low levels of antibiotics present in many environments can select for resistant bacteria, yet the evolutionary pathways for resistance development during exposure to low amounts of antibiotics remain poorly defined. Here we show that Salmonella enterica exposed to sub-MIC levels of streptomycin evolved high-level resistance via novel mechanisms that are different from those observed during lethal selections. During lethal selection only rpsL mutations are found, whereas at sub-MIC selection resistance is generated by several small-effect resistance mutations that combined confer high-level resistance via three different mechanisms: (i) alteration of the ribosomal RNA target (gidB mutations), (ii) reduction in aminoglycoside uptake (cyoB, nuoG, and trkH mutations), and (iii) induction of the aminoglycoside-modifying enzyme AadA (znuA mutations). These results demonstrate how the strength of the selective pressure influences evolutionary trajectories and that even weak selective pressures can cause evolution of high-level resistance.

Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers.

PubMed

Hodgins, Kathryn A; Yeaman, Sam; Nurkowski, Kristin A; Rieseberg, Loren H; Aitken, Sally N

2016-06-01

The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca × engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of synonymous site diversity, and longer proteins than slowly diverging genes. Similar patterns were identified for the untranslated regions, but with some exceptions. We found evidence that genes with low expression levels had a larger fraction of nearly neutral sites, suggesting a primary role for negative selection in determining the association between evolutionary rate and expression level. There was limited evidence for differences in the rate of positive selection among genes with divergent versus conserved expression profiles and some evidence supporting relaxed selection in genes diverging in expression between the species. Finally, we identified a small number of genes that showed evidence of site-specific positive selection using divergence data alone. However, estimates of the proportion of sites fixed by positive selection (α) were in the range of other plant species with large effective population sizes suggesting relatively high rates of adaptive divergence among conifers. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition

PubMed Central

Lefébure, Tristan; Stanhope, Michael J

2007-01-01

Background The genus Streptococcus is one of the most diverse and important human and agricultural pathogens. This study employs comparative evolutionary analyses of 26 Streptococcus genomes to yield an improved understanding of the relative roles of recombination and positive selection in pathogen adaptation to their hosts. Results Streptococcus genomes exhibit extreme levels of evolutionary plasticity, with high levels of gene gain and loss during species and strain evolution. S. agalactiae has a large pan-genome, with little recombination in its core-genome, while S. pyogenes has a smaller pan-genome and much more recombination of its core-genome, perhaps reflecting the greater habitat, and gene pool, diversity for S. agalactiae compared to S. pyogenes. Core-genome recombination was evident in all lineages (18% to 37% of the core-genome judged to be recombinant), while positive selection was mainly observed during species differentiation (from 11% to 34% of the core-genome). Positive selection pressure was unevenly distributed across lineages and biochemical main role categories. S. suis was the lineage with the greatest level of positive selection pressure, the largest number of unique loci selected, and the largest amount of gene gain and loss. Conclusion Recombination is an important evolutionary force in shaping Streptococcus genomes, not only in the acquisition of significant portions of the genome as lineage specific loci, but also in facilitating rapid evolution of the core-genome. Positive selection, although undoubtedly a slower process, has nonetheless played an important role in adaptation of the core-genome of different Streptococcus species to different hosts. PMID:17475002

Making evolutionary biology a basic science for medicine

PubMed Central

Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

2010-01-01

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine.

PubMed

Nesse, Randolph M; Bergstrom, Carl T; Ellison, Peter T; Flier, Jeffrey S; Gluckman, Peter; Govindaraju, Diddahally R; Niethammer, Dietrich; Omenn, Gilbert S; Perlman, Robert L; Schwartz, Mark D; Thomas, Mark G; Stearns, Stephen C; Valle, David

2010-01-26

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease.

Directional selection effects on patterns of phenotypic (co)variation in wild populations.

PubMed

Assis, A P A; Patton, J L; Hubbe, A; Marroig, G

2016-11-30

Phenotypic (co)variation is a prerequisite for evolutionary change, and understanding how (co)variation evolves is of crucial importance to the biological sciences. Theoretical models predict that under directional selection, phenotypic (co)variation should evolve in step with the underlying adaptive landscape, increasing the degree of correlation among co-selected traits as well as the amount of genetic variance in the direction of selection. Whether either of these outcomes occurs in natural populations is an open question and thus an important gap in evolutionary theory. Here, we documented changes in the phenotypic (co)variation structure in two separate natural populations in each of two chipmunk species (Tamias alpinus and T. speciosus) undergoing directional selection. In populations where selection was strongest (those of T. alpinus), we observed changes, at least for one population, in phenotypic (co)variation that matched theoretical expectations, namely an increase of both phenotypic integration and (co)variance in the direction of selection and a re-alignment of the major axis of variation with the selection gradient. © 2016 The Author(s).

Evolution of Site-Selection Stabilizes Population Dynamics, Promotes Even Distribution of Individuals, and Occasionally Causes Evolutionary Suicide.

PubMed

Parvinen, Kalle; Brännström, Åke

2016-08-01

Species that compete for access to or use of sites, such as parasitic mites attaching to honey bees or apple maggots laying eggs in fruits, can potentially increase their fitness by carefully selecting sites at which they face little or no competition. Here, we systematically investigate the evolution of site-selection strategies among animals competing for discrete sites. By developing and analyzing a mechanistic and population-dynamical model of site selection in which searching individuals encounter sites sequentially and can choose to accept or continue to search based on how many conspecifics are already there, we give a complete characterization of the different site-selection strategies that can evolve. We find that evolution of site-selection stabilizes population dynamics, promotes even distribution of individuals among sites, and occasionally causes evolutionary suicide. We also discuss the broader implications of our findings and propose how they can be reconciled with an earlier study (Nonaka et al. in J Theor Biol 317:96-104, 2013) that reported selection toward ever higher levels of aggregation among sites as a consequence of site-selection.

Pumping ions: rapid parallel evolution of ionic regulation following habitat invasions.

PubMed

Lee, Carol Eunmi; Kiergaard, Michael; Gelembiuk, Gregory William; Eads, Brian Donovan; Posavi, Marijan

2011-08-01

Marine to freshwater colonizations constitute among the most dramatic evolutionary transitions in the history of life. This study examined evolution of ionic regulation following saline-to-freshwater transitions in an invasive species. In recent years, the copepod Eurytemora affinis has invaded freshwater habitats multiple times independently. We found parallel evolutionary shifts in ion-motive enzyme activity (V-type H(+) ATPase, Na(+) /K(+) -ATPase) across independent invasions and in replicate laboratory selection experiments. Freshwater populations exhibited increased V-type H(+) ATPase activity in fresh water (0 PSU) and declines at higher salinity (15 PSU) relative to saline populations. This shift represented marked evolutionary increases in plasticity. In contrast, freshwater populations displayed reduced Na(+) /K(+) -ATPase activity across all salinities. Most notably, modifying salinity alone during laboratory selection experiments recapitulated the evolutionary shifts in V-type H(+) ATPase activity observed in nature. Maternal and embryonic acclimation could not account for the observed shifts in enzyme activity. V-type H(+) ATPase function has been hypothesized to be critical for freshwater and terrestrial adaptations, but evolution of this enzyme function had not been previously demonstrated in the context of habitat transitions. Moreover, the speed of these evolutionary shifts was remarkable, within a few generations in the laboratory and a few decades in the wild. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

TARGETED CAPTURE IN EVOLUTIONARY AND ECOLOGICAL GENOMICS

PubMed Central

Jones, Matthew R.; Good, Jeffrey M.

2016-01-01

The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole genome sequencing in ecological and evolutionary genomic studies. High throughput targeted capture is one such strategy that involves the parallel enrichment of pre-selected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across labs focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to 1) increase the accessibility of targeted capture to researchers working in non-model taxa by discussing capture methods that circumvent the need of a reference genome, 2) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy, and 3) discuss the future of targeted capture and other genome partitioning approaches in light of the increasing accessibility of whole genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole genome sequencing. PMID:26137993

Genome-Wide Motif Statistics are Shaped by DNA Binding Proteins over Evolutionary Time Scales

NASA Astrophysics Data System (ADS)

Qian, Long; Kussell, Edo

2016-10-01

The composition of a genome with respect to all possible short DNA motifs impacts the ability of DNA binding proteins to locate and bind their target sites. Since nonfunctional DNA binding can be detrimental to cellular functions and ultimately to organismal fitness, organisms could benefit from reducing the number of nonfunctional DNA binding sites genome wide. Using in vitro measurements of binding affinities for a large collection of DNA binding proteins, in multiple species, we detect a significant global avoidance of weak binding sites in genomes. We demonstrate that the underlying evolutionary process leaves a distinct genomic hallmark in that similar words have correlated frequencies, a signal that we detect in all species across domains of life. We consider the possibility that natural selection against weak binding sites contributes to this process, and using an evolutionary model we show that the strength of selection needed to maintain global word compositions is on the order of point mutation rates. Likewise, we show that evolutionary mechanisms based on interference of protein-DNA binding with replication and mutational repair processes could yield similar results and operate with similar rates. On the basis of these modeling and bioinformatic results, we conclude that genome-wide word compositions have been molded by DNA binding proteins acting through tiny evolutionary steps over time scales spanning millions of generations.

Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes).

PubMed

Hayakawa, Takashi; Sugawara, Tohru; Go, Yasuhiro; Udono, Toshifumi; Hirai, Hirohisa; Imai, Hiroo

2012-01-01

Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires.

Eco-Geographical Diversification of Bitter Taste Receptor Genes (TAS2Rs) among Subspecies of Chimpanzees (Pan troglodytes)

PubMed Central

Hayakawa, Takashi; Sugawara, Tohru; Go, Yasuhiro; Udono, Toshifumi; Hirai, Hirohisa; Imai, Hiroo

2012-01-01

Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires. PMID:22916235

Inferring directions of evolution from patterns of variation: The legacy of Sergei Meyen

PubMed Central

Sharov, Alexei A.; Igamberdiev, Abir U.

2014-01-01

In the era of the Extended Evolutionary Synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935-1987), a paleobotanist who argued that the theory of evolution should incorporate a “nomothetical” approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of “repeated polymorphic sets” (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioural capacities. Meyen's theory is compatible with Darwin's natural selection; however Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviours) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations. PMID:25072709

Current selection for lower migratory activity will drive the evolution of residency in a migratory bird population.

PubMed

Pulido, Francisco; Berthold, Peter

2010-04-20

Global warming is impacting biodiversity by altering the distribution, abundance, and phenology of a wide range of animal and plant species. One of the best documented responses to recent climate change is alterations in the migratory behavior of birds, but the mechanisms underlying these phenotypic adjustments are largely unknown. This knowledge is still crucial to predict whether populations of migratory birds will adapt to a rapid increase in temperature. We monitored migratory behavior in a population of blackcaps (Sylvia atricapilla) to test for evolutionary responses to recent climate change. Using a common garden experiment in time and captive breeding we demonstrated a genetic reduction in migratory activity and evolutionary change in phenotypic plasticity of migration onset. An artificial selection experiment further revealed that residency will rapidly evolve in completely migratory bird populations if selection for shorter migration distance persists. Our findings suggest that current alterations of the environment are favoring birds wintering closer to the breeding grounds and that populations of migratory birds have strongly responded to these changes in selection. The reduction of migratory activity is probably an important evolutionary process in the adaptation of migratory birds to climate change, because it reduces migration costs and facilitates the rapid adjustment to the shifts in the timing of food availability during reproduction.

Characterization of the Avian Trojan Gene Family Reveals Contrasting Evolutionary Constraints

PubMed Central

Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

2015-01-01

“Trojan” is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules. PMID:25803627

Characterization of the avian Trojan gene family reveals contrasting evolutionary constraints.

PubMed

Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

2015-01-01

"Trojan" is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules.

Shaping communicative colour signals over evolutionary time

PubMed Central

Oyola Morales, José R.; Vital-García, Cuauhcihuatl; Hews, Diana K.; Martins, Emília P.

2016-01-01

Many evolutionary forces can shape the evolution of communicative signals, and the long-term impact of each force may depend on relative timing and magnitude. We use a phylogenetic analysis to infer the history of blue belly patches of Sceloporus lizards, and a detailed spectrophotometric analysis of four species to explore the specific forces shaping evolutionary change. We find that the ancestor of Sceloporus had blue patches. We then focus on four species; the first evolutionary shift (captured by comparison of S. merriami and S. siniferus) represents an ancient loss of the belly patch by S. siniferus, and the second evolutionary shift, bounded by S. undulatus and S. virgatus, represents a more recent loss of blue belly patch by S. virgatus. Conspicuousness measurements suggest that the species with the recent loss (S. virgatus) is the least conspicuous. Results for two other species (S. siniferus and S. merriami) suggest that over longer periods of evolutionary time, new signal colours have arisen which minimize absolute contrast with the habitat while maximizing conspicuousness to a lizard receiver. Specifically, males of the species representing an ancient loss of blue patch (S. siniferus) are more conspicuous than are females in the UV, whereas S. merriami males have evolved a green element that makes their belly patches highly sexually dimorphic but no more conspicuous than the white bellies of S. merriami females. Thus, our results suggest that natural selection may act more immediately to reduce conspicuousness, whereas sexual selection may have a more complex impact on communicative signals through the introduction of new colours. PMID:28018661

Shaping communicative colour signals over evolutionary time.

PubMed

Ossip-Drahos, Alison G; Oyola Morales, José R; Vital-García, Cuauhcihuatl; Zúñiga-Vega, J Jaime; Hews, Diana K; Martins, Emília P

2016-11-01

Many evolutionary forces can shape the evolution of communicative signals, and the long-term impact of each force may depend on relative timing and magnitude. We use a phylogenetic analysis to infer the history of blue belly patches of Sceloporus lizards, and a detailed spectrophotometric analysis of four species to explore the specific forces shaping evolutionary change. We find that the ancestor of Sceloporus had blue patches. We then focus on four species; the first evolutionary shift (captured by comparison of S. merriami and S. siniferus ) represents an ancient loss of the belly patch by S. siniferus , and the second evolutionary shift, bounded by S. undulatus and S. virgatus , represents a more recent loss of blue belly patch by S. virgatus . Conspicuousness measurements suggest that the species with the recent loss ( S. virgatus ) is the least conspicuous. Results for two other species ( S. siniferus and S. merriami ) suggest that over longer periods of evolutionary time, new signal colours have arisen which minimize absolute contrast with the habitat while maximizing conspicuousness to a lizard receiver. Specifically, males of the species representing an ancient loss of blue patch ( S. siniferus ) are more conspicuous than are females in the UV, whereas S. merriami males have evolved a green element that makes their belly patches highly sexually dimorphic but no more conspicuous than the white bellies of S. merriami females. Thus, our results suggest that natural selection may act more immediately to reduce conspicuousness, whereas sexual selection may have a more complex impact on communicative signals through the introduction of new colours.

Estimating the ratios of the stationary distribution values for Markov chains modeling evolutionary algorithms.

PubMed

Mitavskiy, Boris; Cannings, Chris

2009-01-01

The evolutionary algorithm stochastic process is well-known to be Markovian. These have been under investigation in much of the theoretical evolutionary computing research. When the mutation rate is positive, the Markov chain modeling of an evolutionary algorithm is irreducible and, therefore, has a unique stationary distribution. Rather little is known about the stationary distribution. In fact, the only quantitative facts established so far tell us that the stationary distributions of Markov chains modeling evolutionary algorithms concentrate on uniform populations (i.e., those populations consisting of a repeated copy of the same individual). At the same time, knowing the stationary distribution may provide some information about the expected time it takes for the algorithm to reach a certain solution, assessment of the biases due to recombination and selection, and is of importance in population genetics to assess what is called a "genetic load" (see the introduction for more details). In the recent joint works of the first author, some bounds have been established on the rates at which the stationary distribution concentrates on the uniform populations. The primary tool used in these papers is the "quotient construction" method. It turns out that the quotient construction method can be exploited to derive much more informative bounds on ratios of the stationary distribution values of various subsets of the state space. In fact, some of the bounds obtained in the current work are expressed in terms of the parameters involved in all the three main stages of an evolutionary algorithm: namely, selection, recombination, and mutation.

Applying ecological and evolutionary theory to cancer: a long and winding road.

PubMed

Thomas, Frédéric; Fisher, Daniel; Fort, Philippe; Marie, Jean-Pierre; Daoust, Simon; Roche, Benjamin; Grunau, Christoph; Cosseau, Céline; Mitta, Guillaume; Baghdiguian, Stephen; Rousset, François; Lassus, Patrice; Assenat, Eric; Grégoire, Damien; Missé, Dorothée; Lorz, Alexander; Billy, Frédérique; Vainchenker, William; Delhommeau, François; Koscielny, Serge; Itzykson, Raphael; Tang, Ruoping; Fava, Fanny; Ballesta, Annabelle; Lepoutre, Thomas; Krasinska, Liliana; Dulic, Vjekoslav; Raynaud, Peggy; Blache, Philippe; Quittau-Prevostel, Corinne; Vignal, Emmanuel; Trauchessec, Hélène; Perthame, Benoit; Clairambault, Jean; Volpert, Vitali; Solary, Eric; Hibner, Urszula; Hochberg, Michael E

2013-01-01

Since the mid 1970s, cancer has been described as a process of Darwinian evolution, with somatic cellular selection and evolution being the fundamental processes leading to malignancy and its many manifestations (neoangiogenesis, evasion of the immune system, metastasis, and resistance to therapies). Historically, little attention has been placed on applications of evolutionary biology to understanding and controlling neoplastic progression and to prevent therapeutic failures. This is now beginning to change, and there is a growing international interest in the interface between cancer and evolutionary biology. The objective of this introduction is first to describe the basic ideas and concepts linking evolutionary biology to cancer. We then present four major fronts where the evolutionary perspective is most developed, namely laboratory and clinical models, mathematical models, databases, and techniques and assays. Finally, we discuss several of the most promising challenges and future prospects in this interdisciplinary research direction in the war against cancer.

Stability-based sorting: The forgotten process behind (not only) biological evolution.

PubMed

Toman, Jan; Flegr, Jaroslav

2017-12-21

Natural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more general persistence principle, whose temporal consequences we propose to name "stability-based sorting" (SBS). Sorting based on static stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities. Sorted entities could originate independently from each other, are not required to propagate and need not exhibit heredity. Natural selection is a specific form of SBS-sorting based on dynamic stability. It requires some form of heredity and is based on competition for the largest difference between the speed of generating its own copies and their expiration. SBS in its strict sense and selection thus have markedly different evolutionary consequences that are stressed in this paper. In contrast to selection, which is opportunistic, SBS is able to accumulate even momentarily detrimental characters that are advantageous for the long-term persistence of sorted entities. However, it lacks the amplification effect based on the preferential propagation of holders of advantageous characters. Thus, it works slower than selection and normally is unable to create complex adaptations. From a long-term perspective, SBS is a decisive force in evolution-especially macroevolution. SBS offers a new explanation for numerous evolutionary phenomena, including broad distribution and persistence of sexuality, altruistic behaviour, horizontal gene transfer, patterns of evolutionary stasis, planetary homeostasis, increasing ecosystem resistance to disturbances, and the universal decline of disparity in the evolution of metazoan lineages. SBS acts on all levels in all biotic and abiotic systems. It could be the only truly universal evolutionary process, and an explanatory framework based on SBS could provide new insight into the evolution of complex abiotic and biotic systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary divergence in sexual signals: Insights from within and among barn swallow populations

NASA Astrophysics Data System (ADS)

Wilkins, Matthew Reed

A wealth of studies across diverse animal groups indicate the importance of sexual selection in shaping phenotypes within and across breeding populations. In recent decades, much research has focused on how divergent sexual selection pressures among populations may lead to speciation. For my first dissertation chapter, I performed a literature review on the causes and consequences of evolutionary divergence in acoustic signals and developed the acoustic window conceptual framework for understanding the contributions of selection, genetic drift, and evolutionary constraint to signal divergence. Further, I found that sexual selection explains acoustic differences between recently diverged populations of the best-studied taxa. However, the relative contributions of ecological selection, sexual selection, and drift to acoustic divergence have not typically been considered within the same study systems. The remainder of my dissertation used the Northern Hemisphere-distributed barn swallow ( Hirundo rustica) species complex as a model system to study sender-receiver dynamics, intra- and intersexual selection pressures, and visual and acoustic signal interactions at the local scale, and signal divergence across populations at the global scale. From song recordings taken across 19 sampling sites, spanning five of six described subspecies, I demonstrated considerable conservation in song structure. However, temporal traits were highly divergent across subspecies, and in particular, the speed of the terminal trill of songs. In a detailed study of the multimodal communication system of the barn swallow (including visual and acoustic traits), I demonstrated that males and females use different types of signals to mediate competition and mate choice. One of the only exceptions to this rule was trill rate, which was also implicated in song divergence across populations. In order to test the function of trill rate in communication, I performed a two-year playback study within the North American subspecies, H. r. erythrogaster. Contrary to expectations, males did not have stronger responses to faster trilling (high performance) simulated intruders. Instead, resident males had stronger responses to the high performance stimulus only when the intruder was also darker than the resident. Collectively, my dissertation offers novel insight into the evolutionary dynamics of complex sexual signaling at multiple spatial scales.

Multivariate selection and intersexual genetic constraints in a wild bird population.

PubMed

Poissant, J; Morrissey, M B; Gosler, A G; Slate, J; Sheldon, B C

2016-10-01

When selection differs between the sexes for traits that are genetically correlated between the sexes, there is potential for the effect of selection in one sex to be altered by indirect selection in the other sex, a situation commonly referred to as intralocus sexual conflict (ISC). While potentially common, ISC has rarely been studied in wild populations. Here, we studied ISC over a set of morphological traits (wing length, tarsus length, bill depth and bill length) in a wild population of great tits (Parus major) from Wytham Woods, UK. Specifically, we quantified the microevolutionary impacts of ISC by combining intra- and intersex additive genetic (co)variances and sex-specific selection estimates in a multivariate framework. Large genetic correlations between homologous male and female traits combined with evidence for sex-specific multivariate survival selection suggested that ISC could play an appreciable role in the evolution of this population. Together, multivariate sex-specific selection and additive genetic (co)variance for the traits considered accounted for additive genetic variance in fitness that was uncorrelated between the sexes (cross-sex genetic correlation = -0.003, 95% CI = -0.83, 0.83). Gender load, defined as the reduction in a population's rate of adaptation due to sex-specific effects, was estimated at 50% (95% CI = 13%, 86%). This study provides novel insights into the evolution of sexual dimorphism in wild populations and illustrates how quantitative genetics and selection analyses can be combined in a multivariate framework to quantify the microevolutionary impacts of ISC. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Sexual selection predicts brain structure in dragon lizards.

PubMed

Hoops, D; Ullmann, J F P; Janke, A L; Vidal-Garcia, M; Stait-Gardner, T; Dwihapsari, Y; Merkling, T; Price, W S; Endler, J A; Whiting, M J; Keogh, J S

2017-02-01

Phenotypic traits such as ornaments and armaments are generally shaped by sexual selection, which often favours larger and more elaborate males compared to females. But can sexual selection also influence the brain? Previous studies in vertebrates report contradictory results with no consistent pattern between variation in brain structure and the strength of sexual selection. We hypothesize that sexual selection will act in a consistent way on two vertebrate brain regions that directly regulate sexual behaviour: the medial preoptic nucleus (MPON) and the ventromedial hypothalamic nucleus (VMN). The MPON regulates male reproductive behaviour whereas the VMN regulates female reproductive behaviour and is also involved in male aggression. To test our hypothesis, we used high-resolution magnetic resonance imaging combined with traditional histology of brains in 14 dragon lizard species of the genus Ctenophorus that vary in the strength of precopulatory sexual selection. Males belonging to species that experience greater sexual selection had a larger MPON and a smaller VMN. Conversely, females did not show any patterns of variation in these brain regions. As the volumes of both these regions also correlated with brain volume (BV) in our models, we tested whether they show the same pattern of evolution in response to changes in BV and found that the do. Therefore, we show that the primary brain nuclei underlying reproductive behaviour in vertebrates can evolve in a mosaic fashion, differently between males and females, likely in response to sexual selection, and that these same regions are simultaneously evolving in concert in relation to overall brain size. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Evolutionary analysis of Old World arenaviruses reveals a major adaptive contribution of the viral polymerase.

PubMed

Pontremoli, Chiara; Forni, Diego; Cagliani, Rachele; Pozzoli, Uberto; Riva, Stefania; Bravo, Ignacio G; Clerici, Mario; Sironi, Manuela

2017-10-01

The Old World (OW) arenavirus complex includes several species of rodent-borne viruses, some of which (i.e., Lassa virus, LASV and Lymphocytic choriomeningitis virus, LCMV) cause human diseases. Most LCMV and LASV infections are caused by rodent-to-human transmissions. Thus, viral evolution is largely determined by events that occur in the wildlife reservoirs. We used a set of human- and rodent-derived viral sequences to investigate the evolutionary history underlying OW arenavirus speciation, as well as the more recent selective events that accompanied LASV spread in West Africa. We show that the viral RNA polymerase (L protein) was a major positive selection target in OW arenaviruses and during LASV out-of-Nigeria migration. No evidence of selection was observed for the glycoprotein, whereas positive selection acted on the nucleoprotein (NP) during LCMV speciation. Positively selected sites in L and NP are surrounded by highly conserved residues, and the bulk of the viral genome evolves under purifying selection. Several positively selected sites are likely to modulate viral replication/transcription. In both L and NP, structural features (solvent exposed surface area) are important determinants of site-wise evolutionary rate variation. By incorporating several rodent-derived sequences, we also performed an analysis of OW arenavirus codon adaptation to the human host. Results do not support a previously hypothesized role of codon adaptation in disease severity for non-Nigerian strains. In conclusion, L and NP represent the major selection targets and possible determinants of disease presentation; these results suggest that field surveys and experimental studies should primarily focus on these proteins. © 2017 John Wiley & Sons Ltd.

The evolution of colour polymorphism in British winter-active Lepidoptera in response to search image use by avian predators.

PubMed

Weir, Jamie C

2018-05-10

Phenotypic polymorphism in cryptic species is widespread. This may evolve in response to search image use by predators exerting negative frequency-dependent selection on intraspecific colour morphs, 'apostatic selection'. Evidence exists to indicate search image formation by predators and apostatic selection operating on wild prey populations, though not to demonstrate search image use directly resulting in apostatic selection. The present study attempted to address this deficiency, using British Lepidoptera active in winter as a model system. It has been proposed that the typically polymorphic wing colouration of these species represents an anti-search image adaptation against birds. To test (a) for search image-driven apostatic selection, dimorphic populations of artificial moth-like models were established in woodland at varying relative morph frequencies and exposed to predation by natural populations of birds. In addition, to test (b) whether abundance and degree of polymorphism are correlated across British winter-active moths, as predicted where search image use drives apostatic selection, a series of phylogenetic comparative analyses were conducted. There was a positive relationship between artificial morph frequency and probability of predation, consistent with birds utilizing search images and exerting apostatic selection. Abundance and degree of polymorphism were found to be positively correlated across British Lepidoptera active in winter, though not across all taxonomic groups analysed. This evidence is consistent with polymorphism in this group having evolved in response to search image-driven apostatic selection and supports the viability of this mechanism as a means by which phenotypic and genetic variation may be maintained in natural populations. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Serotonin, behavior, and natural selection in New World monkeys.

PubMed

Reales, Guillermo; Paixão-Côrtes, Vanessa R; Cybis, Gabriela B; Gonçalves, Gislene L; Pissinatti, Alcides; Salzano, Francisco M; Bortolini, Maria CÁtira

2018-06-26

Traits that undergo massive natural selection pressure, with multiple events of positive selection, are hard to find. Social behaviour, in social animals, is crucial for survival, and genetic networks involved in behaviour, such as those of serotonin (5-HT) and other neurotransmitters, must be the target of natural selection. Here, we used molecular analyses to search for signals of positive selection in the 5-HT system and found such signals in the M3-M4 intracellular domain of the 5-HT3A serotonin receptor subunit (HTR3A) in primates. We detected four amino acid sites with signs of putatively positive selection (398, 403, 432 and 416); the first three showed indications of being selected in New World monkeys (NWM, Platyrrhini), specifically in the Callitrichinae branch. Additionally, we searched for associations of these amino acid variants with social behavioural traits (i.e. sex-biased dispersal, dominance and social monogamy) using classical and Bayesian methods, and found statistically significant associations for unbiased sex dispersal (398L and 416S), unbiased sex dominance (416S) and social monogamy (416S), as well as significant positive correlation between female dispersal and 403G. Furthermore, we found putatively functional protein motifs determined by three selected sites, of which we highlight a ligand motif to GSK3 in the 416S variant, appearing only in Platyrrhini. 5-HT, 5-HT3A receptor and GSK3 are part of a network that participates in neurodevelopment and regulates behaviour, among other functions. We suggest that these genetic variations, together with those found in other neurotransmitter systems, must contribute to adaptive behaviours and consequently to fitness in NWMs. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Comparison of some evolutionary algorithms for optimization of the path synthesis problem

NASA Astrophysics Data System (ADS)

Grabski, Jakub Krzysztof; Walczak, Tomasz; Buśkiewicz, Jacek; Michałowska, Martyna

2018-01-01

The paper presents comparison of the results obtained in a mechanism synthesis by means of some selected evolutionary algorithms. The optimization problem considered in the paper as an example is the dimensional synthesis of the path generating four-bar mechanism. In order to solve this problem, three different artificial intelligence algorithms are employed in this study.

Darwinian evolution in the light of genomics

PubMed Central

Koonin, Eugene V.

2009-01-01

Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future. PMID:19213802

Predator confusion is sufficient to evolve swarming behaviour

PubMed Central

Olson, Randal S.; Hintze, Arend; Dyer, Fred C.; Knoester, David B.; Adami, Christoph

2013-01-01

Swarming behaviours in animals have been extensively studied owing to their implications for the evolution of cooperation, social cognition and predator–prey dynamics. An important goal of these studies is discerning which evolutionary pressures favour the formation of swarms. One hypothesis is that swarms arise because the presence of multiple moving prey in swarms causes confusion for attacking predators, but it remains unclear how important this selective force is. Using an evolutionary model of a predator–prey system, we show that predator confusion provides a sufficient selection pressure to evolve swarming behaviour in prey. Furthermore, we demonstrate that the evolutionary effect of predator confusion on prey could in turn exert pressure on the structure of the predator's visual field, favouring the frontally oriented, high-resolution visual systems commonly observed in predators that feed on swarming animals. Finally, we provide evidence that when prey evolve swarming in response to predator confusion, there is a change in the shape of the functional response curve describing the predator's consumption rate as prey density increases. Thus, we show that a relatively simple perceptual constraint—predator confusion—could have pervasive evolutionary effects on prey behaviour, predator sensory mechanisms and the ecological interactions between predators and prey. PMID:23740485

Predator confusion is sufficient to evolve swarming behaviour.

PubMed

Olson, Randal S; Hintze, Arend; Dyer, Fred C; Knoester, David B; Adami, Christoph

2013-08-06

Swarming behaviours in animals have been extensively studied owing to their implications for the evolution of cooperation, social cognition and predator-prey dynamics. An important goal of these studies is discerning which evolutionary pressures favour the formation of swarms. One hypothesis is that swarms arise because the presence of multiple moving prey in swarms causes confusion for attacking predators, but it remains unclear how important this selective force is. Using an evolutionary model of a predator-prey system, we show that predator confusion provides a sufficient selection pressure to evolve swarming behaviour in prey. Furthermore, we demonstrate that the evolutionary effect of predator confusion on prey could in turn exert pressure on the structure of the predator's visual field, favouring the frontally oriented, high-resolution visual systems commonly observed in predators that feed on swarming animals. Finally, we provide evidence that when prey evolve swarming in response to predator confusion, there is a change in the shape of the functional response curve describing the predator's consumption rate as prey density increases. Thus, we show that a relatively simple perceptual constraint--predator confusion--could have pervasive evolutionary effects on prey behaviour, predator sensory mechanisms and the ecological interactions between predators and prey.

Natural history collections as windows on evolutionary processes.

PubMed

Holmes, Michael W; Hammond, Talisin T; Wogan, Guinevere O U; Walsh, Rachel E; LaBarbera, Katie; Wommack, Elizabeth A; Martins, Felipe M; Crawford, Jeremy C; Mack, Katya L; Bloch, Luke M; Nachman, Michael W

2016-02-01

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the laboratory, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short timescales in response to presumably strong selective pressures. In some instances, evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations. © 2016 John Wiley & Sons Ltd.

Evolutionary potential of upper thermal tolerance: biogeographic patterns and expectations under climate change.

PubMed

Diamond, Sarah E

2017-02-01

How will organisms respond to climate change? The rapid changes in global climate are expected to impose strong directional selection on fitness-related traits. A major open question then is the potential for adaptive evolutionary change under these shifting climates. At the most basic level, evolutionary change requires the presence of heritable variation and natural selection. Because organismal tolerances of high temperature place an upper bound on responding to temperature change, there has been a surge of research effort on the evolutionary potential of upper thermal tolerance traits. Here, I review the available evidence on heritable variation in upper thermal tolerance traits, adopting a biogeographic perspective to understand how heritability of tolerance varies across space. Specifically, I use meta-analytical models to explore the relationship between upper thermal tolerance heritability and environmental variability in temperature. I also explore how variation in the methods used to obtain these thermal tolerance heritabilities influences the estimation of heritable variation in tolerance. I conclude by discussing the implications of a positive relationship between thermal tolerance heritability and environmental variability in temperature and how this might influence responses to future changes in climate. © 2016 New York Academy of Sciences.

Genome-Wide Motif Statistics are Shaped by DNA Binding Proteins over Evolutionary Time Scales

NASA Astrophysics Data System (ADS)

Qian, Long; Kussell, Edo

The composition of genomes with respect to short DNA motifs impacts the ability of DNA binding proteins to locate and bind their target sites. Since nonfunctional DNA binding can be detrimental to cellular functions and ultimately to organismal fitness, organisms could benefit from reducing the number of nonfunctional binding sites genome wide. Using in vitro measurements of binding affinities for a large collection of DNA binding proteins, in multiple species, we detect a significant global avoidance of weak binding sites in genomes. The underlying evolutionary process leaves a distinct genomic hallmark in that similar words have correlated frequencies, which we detect in all species across domains of life. We hypothesize that natural selection against weak binding sites contributes to this process, and using an evolutionary model we show that the strength of selection needed to maintain global word compositions is on the order of point mutation rates. Alternative contributions may come from interference of protein-DNA binding with replication and mutational repair processes, which operates with similar rates. We conclude that genome-wide word compositions have been molded by DNA binding proteins through tiny evolutionary steps over timescales spanning millions of generations.

A model of ecological and evolutionary consequences of color polymorphism.

PubMed

Forsman, Anders; Ahnesjö, Jonas; Caesar, Sofia; Karlsson, Magnus

2008-01-01

We summarize direct and indirect effects on fitness components of animal color pattern and present a synthesis of theories concerning the ecological and evolutionary dynamics of chromatic multiple niche polymorphisms. Previous endeavors have aimed primarily at identifying conditions that promote the evolution and maintenance of polymorphisms. We consider in a conceptual model also the reciprocal influence of color polymorphism on population processes and propose that polymorphism entails selective advantages that may promote the ecological success of polymorphic species. The model begins with an evolutionary branching event from mono- to polymorphic condition that, under the influence of correlational selection, is predicted to promote the evolution of physical integration of coloration and other traits (cf. multi-trait coevolution and complex phenotypes). We propose that the coexistence within a population of alternative ecomorphs with coadapted gene complexes promotes utilization of diverse environmental resources, population stability and persistence, colonization success, and range expansions, and enhances the evolutionary potential and speciation. Conversely, we predict polymorphic populations to be less vulnerable to environmental change and at lower risk of range contractions and extinctions compared with monomorphic populations. We offer brief suggestions as to how these falsifiable predictions may be tested.

Epidemiological, evolutionary and co-evolutionary implications of context-dependent parasitism

PubMed Central

Vale, Pedro F.; Wilson, Alastair J.; Best, Alex; Boots, Mike; Little, Tom J.

2013-01-01

Victims of infection are expected to suffer increasingly as parasite population growth increases. Yet, under some conditions, faster growing parasites do not appear to cause more damage and infections can be quite tolerable. We studied these conditions by assessing how the relationship between parasite population growth and host health is sensitive to environmental variation. In experimental infections of the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa we show how easily an interaction can shift from a severe interaction, i.e. when host fitness declines substantially with each unit of parasite growth, to a tolerable relationship by changing only simple environmental variables: temperature and food availability. We explored the evolutionary and epidemiological implications of such a shift by modelling pathogen evolution and disease spread under different levels of infection severity, and find that environmental shifts that promote tolerance ultimately result in populations harbouring more parasitized individuals. We also find that the opportunity for selection, as indicated by the variance around traits, varied considerably with the environmental treatment. Thus our results suggest two mechanisms that could underlie co-evolutionary hot- and coldspots: spatial variation in tolerance and spatial variation in the opportunity for selection. PMID:21460572

Natural history collections as windows on evolutionary processes

PubMed Central

Holmes, Michael W.; Hammond, Talisin T.; Wogan, Guinevere O.U.; Walsh, Rachel E.; LaBarbera, Katie; Wommack, Elizabeth A.; Martins, Felipe M.; Crawford, Jeremy C.; Mack, Katya L.; Bloch, Luke M.; Nachman, Michael W.

2016-01-01

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics, and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the lab, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short time scales in response to presumably strong selective pressures. In some instances evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations. PMID:26757135

Phenological shifts in North American red squirrels: disentangling the roles of phenotypic plasticity and microevolution.

PubMed

Lane, Jeffrey E; McAdam, Andrew G; McFarlane, S Eryn; Williams, Cory T; Humphries, Murray M; Coltman, David W; Gorrell, Jamieson C; Boutin, Stan

2018-06-01

Phenological shifts are the most widely reported ecological responses to climate change, but the requirements to distinguish their causes (i.e. phenotypic plasticity vs. microevolution) are rarely met. To do so, we analysed almost two decades of parturition data from a wild population of North American red squirrels (Tamiasciurus hudsonicus). Although an observed advance in parturition date during the first decade provided putative support for climate change-driven microevolution, a closer look revealed a more complex pattern. Parturition date was heritable [h 2  = 0.14 (0.07-0.21 (HPD interval)] and under phenotypic selection [β = -0.14 ± 0.06 (SE)] across the full study duration. However, the early advance reversed in the second decade. Further, selection did not act on the genetic contribution to variation in parturition date, and observed changes in predicted breeding values did not exceed those expected due to genetic drift. Instead, individuals responded plastically to environmental variation, and high food [white spruce (Picea glauca) seed] production in the first decade appears to have produced a plastic advance. In addition, there was little evidence of climate change affecting the advance, as there was neither a significant influence of spring temperature on parturition date or evidence of a change in spring temperatures across the study duration. Heritable traits not responding to selection in accordance with quantitative genetic predictions have long presented a puzzle to evolutionary ecologists. Our results on red squirrels provide empirical support for one potential solution: phenotypic selection arising from an environmental, as opposed to genetic, covariance between the phenotypic trait and annual fitness. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Genome-Wide Analysis of PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) Genes in Plants Reveals the Eudicot-Wide PDAT Gene Expansion and Altered Selective Pressures Acting on the Core Eudicot PDAT Paralogs1[OPEN

PubMed Central

Pan, Xue; Peng, Fred Y.; Weselake, Randall J.

2015-01-01

PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) is an enzyme that catalyzes the transfer of a fatty acyl moiety from the sn-2 position of a phospholipid to the sn-3-position of sn-1,2-diacylglyerol, thus forming triacylglycerol and a lysophospholipid. Although the importance of PDAT in triacylglycerol biosynthesis has been illustrated in some previous studies, the evolutionary relationship of plant PDATs has not been studied in detail. In this study, we investigated the evolutionary relationship of the PDAT gene family across the green plants using a comparative phylogenetic framework. We found that the PDAT candidate genes are present in all examined green plants, including algae, lowland plants (a moss and a lycophyte), monocots, and eudicots. Phylogenetic analysis revealed the evolutionary division of the PDAT gene family into seven major clades. The separation is supported by the conservation and variation in the gene structure, protein properties, motif patterns, and/or selection constraints. We further demonstrated that there is a eudicot-wide PDAT gene expansion, which appears to have been mainly caused by the eudicot-shared ancient gene duplication and subsequent species-specific segmental duplications. In addition, selection pressure analyses showed that different selection constraints have acted on three core eudicot clades, which might enable paleoduplicated PDAT paralogs to either become nonfunctionalized or develop divergent expression patterns during evolution. Overall, our study provides important insights into the evolution of the plant PDAT gene family and explores the evolutionary mechanism underlying the functional diversification among the core eudicot PDAT paralogs. PMID:25585619

The evolutionary ecology of the Lygaeidae

PubMed Central

Burdfield-Steel, Emily R; Shuker, David M

2014-01-01

The Lygaeidae (sensu lato) are a highly successful family of true bugs found worldwide, yet many aspects of their ecology and evolution remain obscure or unknown. While a few species have attracted considerable attention as model species for the study of insect physiology, it is only relatively recently that biologists have begun to explore aspects of their behavior, life history evolution, and patterns of intra- and interspecific ecological interactions across more species. As a result though, a range of new phenotypes and opportunities for addressing current questions in evolutionary ecology has been uncovered. For example, researchers have revealed hitherto unexpectedly rich patterns of bacterial symbiosis, begun to explore the evolutionary function of the family's complex genitalia, and also found evidence of parthenogenesis. Here we review our current understanding of the biology and ecology of the group as a whole, focusing on several of the best-studied characteristics of the group, including aposematism (i.e., the evolution of warning coloration), chemical communication, sexual selection (especially, postcopulatory sexual selection), sexual conflict, and patterns of host-endosymbiont coevolution. Importantly, many of these aspects of lygaeid biology are likely to interact, offering new avenues for research, for instance into how the evolution of aposematism influences sexual selection. With the growing availability of genomic tools for previously “non-model” organisms, combined with the relative ease of keeping many of the polyphagous species in the laboratory, we argue that these bugs offer many opportunities for behavioral and evolutionary ecologists. PMID:25360267

Similar patterns of frequency-dependent selection on animal personalities emerge in three species of social spiders.

PubMed

Lichtenstein, J L L; Pruitt, J N

2015-06-01

Frequency-dependent selection is thought to be a major contributor to the maintenance of phenotypic variation. We tested for frequency-dependent selection on contrasting behavioural strategies, termed here 'personalities', in three species of social spiders, each thought to represent an independent evolutionary origin of sociality. The evolution of sociality in the spider genus Anelosimus is consistently met with the emergence of two temporally stable discrete personality types: an 'aggressive' or 'docile' form. We assessed how the foraging success of each phenotype changes as a function of its representation within a colony. We did this by creating experimental colonies of various compositions (six aggressives, three aggressives and three dociles, one aggressive and five dociles, six dociles), maintaining them in a common garden for 3 weeks, and tracking the mass gained by individuals of either phenotype. We found that both the docile and aggressive phenotypes experienced their greatest mass gain in mixed colonies of mostly docile individuals. However, the performance of both phenotypes decreased as the frequency of the aggressive phenotype increased. Nearly identical patterns of phenotype-specific frequency dependence were recovered in all three species. Naturally occurring colonies of these spiders exhibit mixtures dominated by the docile phenotype, suggesting that these spiders may have evolved mechanisms to maintain the compositions that maximize the success of the colony without compromising the expected reproductive output of either phenotype. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

The evolution of life-history variation in fishes, with particular reference to flatfishes

NASA Astrophysics Data System (ADS)

Roff, Derek A.

This paper explores four aspects of the evolution of life-history variation in fish, with particular reference to the flatfishes: 1. genetic variation and evolutionary response; 2. the size and age at first reproduction; 3. adult lifespan and variation in recruitment; 4. the relationship between reproductive effort and age. Evolutionary response may be limited by previous evolutionary pathways (phylogenetic variation) or by lack of genetic variation due to selection for a single trait. Estimates of heritability suggest, as predicted, that selection is stronger on life-history traits than morphological traits; but there is still adequate genetic variation to permit fairly rapid evolutionary changes. Several approaches to the analysis of the optimal age and size at first reproduction are discussed in the light of a general life-history model based on the assumption that natural selection maximizes r or R 0. It is concluded that one of the most important areas of future research is the relationship between reproduction and mortality. Murphy's hypothesis that the reproductive lifespan should increase with variation in spawning success is shown to be incorrect for fish, at least at the level of interspecific comparison. The model of Charlesworth & León predicting the sufficient condition for reproductive effort to increase with age is tested: in 28 of 31 cases the model predicts an increase of reproductive effort with age. These results suggest that, in general, reproductive effort should increase with age in fish. This prediction is confirmed in the 15 species for which adequate data exist.

Agricultural management affects evolutionary processes in a migratory songbird

USGS Publications Warehouse

Perlut, N.G.; Freeman-Gallant, C. R.; Strong, A.M.; Donovan, T.M.; Kilpatrick, C.W.; Zalik, N.J.

2008-01-01

Hay harvests have detrimental ecological effects on breeding songbirds, as harvesting results in nest failure. Importantly, whether harvesting also affects evolutionary processes is not known. We explored how hay harvest affected social and genetic mating patterns, and thus, the overall opportunity for sexual selection and evolutionary processes for a ground-nesting songbird, the Savannah sparrow (Passerculus sandwichensis). On an unharvested field, 55% of females were in polygynous associations, and social polygyny was associated with greater rates of extra-pair paternity (EPP). In this treatment, synchrony explained variation in EPP rates, as broods by more synchronous females had more EPP than broods by asynchronous females. In contrast, on a harvested field, simultaneous nest failure caused by haying dramatically decreased the overall incidence of EPP by increasing the occurrence of social monogamy and, apparently, the ability of polygynous males to maintain paternity in their own nests. Despite increased social and genetic monogamy, these haying-mediated changes in mating systems resulted in greater than twofold increase in the opportunity for sexual selection. This effect arose, in part, from a 30% increase in the variance associated with within-pair fertilization success, relative to the unharvested field. This effect was caused by a notable increase (+110%) in variance associated with the quality of social mates following simultaneous nest failure. Because up to 40% of regional habitat is harvested by early June, these data may demonstrate a strong population-level effect on mating systems, sexual selection, and consequently, evolutionary processes. ?? 2008 The Authors.

Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network.

PubMed

Sikkink, Kristin L; Reynolds, Rose M; Cresko, William A; Phillips, Patrick C

2015-05-01

Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of covariation in the evolutionary response between phenotypes or across environments differed depending on the environment in which selection occurred, including asymmetrical responses to selection in some cases. These results indicate that variation in pleiotropy across the stress response network is highly sensitive to the external environment. Our findings highlight the complexity of the interaction between genes and environment that influences the ability of organisms to acclimate to novel environments. They also make clear the need to identify the underlying genetic basis of genetic correlations in order understand how patterns of pleiotropy are distributed across complex genetic networks. © 2015 The Author(s).

Signatures of sex-antagonistic selection on recombining sex chromosomes.

PubMed

Kirkpatrick, Mark; Guerrero, Rafael F

2014-06-01

Sex-antagonistic (SA) selection has major evolutionary consequences: it can drive genomic change, constrain adaptation, and maintain genetic variation for fitness. The recombining (or pseudoautosomal) regions of sex chromosomes are a promising setting in which to study SA selection because they tend to accumulate SA polymorphisms and because recombination allows us to deploy the tools of molecular evolution to locate targets of SA selection and quantify evolutionary forces. Here we use coalescent models to characterize the patterns of polymorphism expected within and divergence between recombining X and Y (or Z and W) sex chromosomes. SA selection generates peaks of divergence between X and Y that can extend substantial distances away from the targets of selection. Linkage disequilibrium between neutral sites is also inflated. We show how the pattern of divergence is altered when the SA polymorphism or the sex-determining region was recently established. We use data from the flowering plant Silene latifolia to illustrate how the strength of SA selection might be quantified using molecular data from recombining sex chromosomes. Copyright © 2014 by the Genetics Society of America.

Evolutionary responses of tree phenology to the combined effects of assortative mating, gene flow and divergent selection

PubMed Central

Soularue, J-P; Kremer, A

2014-01-01

The timing of bud burst (TBB) in temperate trees is a key adaptive trait, the expression of which is triggered by temperature gradients across the landscape. TBB is strongly correlated with flowering time and is therefore probably mediated by assortative mating. We derived theoretical predictions and realized numerical simulations of evolutionary changes in TBB in response to divergent selection and gene flow in a metapopulation. We showed that the combination of the environmental gradient of TBB and assortative mating creates contrasting genetic clines, depending on the direction of divergent selection. If divergent selection acts in the same direction as the environmental gradient (cogradient settings), genetic clines are established and inflated by assortative mating. Conversely, under divergent selection of the same strength but acting in the opposite direction (countergradient selection), genetic clines are slightly constrained. We explored the consequences of these dynamics for population maladaptation, by monitoring pollen swamping. Depending on the direction of divergent selection with respect to the environmental gradient, pollen filtering owing to assortative mating either facilitates or impedes adaptation in peripheral populations. PMID:24924591

Mate choice theory and the mode of selection in sexual populations.

PubMed

Carson, Hampton L

2003-05-27

Indirect new data imply that mate and/or gamete choice are major selective forces driving genetic change in sexual populations. The system dictates nonrandom mating, an evolutionary process requiring both revised genetic theory and new data on heritability of characters underlying Darwinian fitness. Successfully reproducing individuals represent rare selections from among vigorous, competing survivors of preadult natural selection. Nonrandom mating has correlated demographic effects: reduced effective population size, inbreeding, low gene flow, and emphasis on deme structure. Characters involved in choice behavior at reproduction appear based on quantitative trait loci. This variability serves selection for fitness within the population, having only an incidental relationship to the origin of genetically based reproductive isolation between populations. The claim that extensive hybridization experiments with Drosophila indicate that selection favors a gradual progression of "isolating mechanisms" is flawed, because intra-group random mating is assumed. Over deep time, local sexual populations are strong, independent genetic systems that use rich fields of variable polygenic components of fitness. The sexual reproduction system thus particularizes, in small subspecific populations, the genetic basis of the grand adaptive sweep of selective evolutionary change, much as Darwin proposed.

Substitution rate and natural selection in parvovirus B19

PubMed Central

Stamenković, Gorana G.; Ćirković, Valentina S.; Šiljić, Marina M.; Blagojević, Jelena V.; Knežević, Aleksandra M.; Joksić, Ivana D.; Stanojević, Maja P.

2016-01-01

The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973–2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1.03 (0.6–1.27) x 10−4 substitutions/site/year, with higher values for analyzed genome partitions. In spite of the highest evolutionary rate, VP2 codons were found to be under purifying selection with rare episodic positive selection, whereas codons under diversifying selection were found in the unique part of VP1, known to contain B19 immune epitopes important in persistent infection. Analyses of overlapping gene regions identified nucleotide positions under opposite selective pressure in different ORFs, suggesting complex evolutionary mechanisms of nucleotide changes in B19 viral genomes. PMID:27775080

ENVIRONMENTALLY INDUCED CHANGES IN CORRELATED RESPONSES TO SELECTION REVEAL VARIABLE PLEIOTROPY ACROSS A COMPLEX GENETIC NETWORK

PubMed Central

Sikkink, Kristin L.; Reynolds, Rose M.; Cresko, William A.; Phillips, Patrick C.

2017-01-01

Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of covariation in the evolutionary response between phenotypes or across environments differed depending on the environment in which selection occurred, including asymmetrical responses to selection in some cases. These results indicate that variation in pleiotropy across the stress response network is highly sensitive to the external environment. Our findings highlight the complexity of the interaction between genes and environment that influences the ability of organisms to acclimate to novel environments. They also make clear the need to identify the underlying genetic basis of genetic correlations in order understand how patterns of pleiotropy are distributed across complex genetic networks. PMID:25809411

How Life History Can Sway the Fixation Probability of Mutants

PubMed Central

Li, Xiang-Yi; Kurokawa, Shun; Giaimo, Stefano; Traulsen, Arne

2016-01-01

In this work, we study the effects of demographic structure on evolutionary dynamics when selection acts on reproduction, survival, or both. In contrast to the previously discovered pattern that the fixation probability of a neutral mutant decreases while the population becomes younger, we show that a mutant with a constant selective advantage may have a maximum or a minimum of the fixation probability in populations with an intermediate fraction of young individuals. This highlights the importance of life history and demographic structure in studying evolutionary dynamics. We also illustrate the fundamental differences between selection on reproduction and selection on survival when age structure is present. In addition, we evaluate the relative importance of size and structure of the population in determining the fixation probability of the mutant. Our work lays the foundation for also studying density- and frequency-dependent effects in populations when demographic structures cannot be neglected. PMID:27129737

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

PubMed Central

Offman, Marc N; Tournier, Alexander L; Bates, Paul A

2008-01-01

Background Automatic protein modelling pipelines are becoming ever more accurate; this has come hand in hand with an increasingly complicated interplay between all components involved. Nevertheless, there are still potential improvements to be made in template selection, refinement and protein model selection. Results In the context of an automatic modelling pipeline, we analysed each step separately, revealing several non-intuitive trends and explored a new strategy for protein conformation sampling using Genetic Algorithms (GA). We apply the concept of alternating evolutionary pressure (AEP), i.e. intermediate rounds within the GA runs where unrestrained, linear growth of the model populations is allowed. Conclusion This approach improves the overall performance of the GA by allowing models to overcome local energy barriers. AEP enabled the selection of the best models in 40% of all targets; compared to 25% for a normal GA. PMID:18673557

Mutation-selection equilibrium in games with multiple strategies.

PubMed

Antal, Tibor; Traulsen, Arne; Ohtsuki, Hisashi; Tarnita, Corina E; Nowak, Martin A

2009-06-21

In evolutionary games the fitness of individuals is not constant but depends on the relative abundance of the various strategies in the population. Here we study general games among n strategies in populations of large but finite size. We explore stochastic evolutionary dynamics under weak selection, but for any mutation rate. We analyze the frequency dependent Moran process in well-mixed populations, but almost identical results are found for the Wright-Fisher and Pairwise Comparison processes. Surprisingly simple conditions specify whether a strategy is more abundant on average than 1/n, or than another strategy, in the mutation-selection equilibrium. We find one condition that holds for low mutation rate and another condition that holds for high mutation rate. A linear combination of these two conditions holds for any mutation rate. Our results allow a complete characterization of nxn games in the limit of weak selection.

Sexually transmitted infection and the evolution of serial monogamy

PubMed Central

McLeod, David V.; Day, Troy

2014-01-01

The selective forces shaping mating systems have long been of interest to biologists. One particular selective pressure that has received comparatively little attention is sexually transmitted infections (STIs). While it has been hypothesized that STIs could drive the evolutionary emergence of monogamy, there is little theoretical support. Here we use an evolutionary invasion analysis to determine what aspects of pathogen virulence and transmission are necessary for serial monogamy to evolve in a promiscuous population. We derive a biologically intuitive invasion condition in terms of population-specific quantities. From this condition, we obtain two main results. First, when pathogen virulence causes mortality rather than sterility, monogamy is more likely to evolve. Second, we find that at intermediate pathogen transmission rates, monogamy is the most selectively advantageous, whereas at high- and low-transmission rates, monogamy is generally selected against. As a result, it is possible for a pathogen to be highly virulent, yet for promiscuity to persist. PMID:25320174

Enemy targeting, trade-offs, and the evolutionary assembly of a tortoise beetle defense arsenal

USDA-ARS?s Scientific Manuscript database

In response to intense enemy selection, immature folivorous insects have evolved elaborate, multi-trait defense arsenals. How enemies foster trait diversification and arsenal assembly depends on which selective mode they impose: whether different enemies select for the same defense or exert conflict...

(Evolutionary) Theories of warfare in preindustrial (foraging) societies.

PubMed

van der Dennen, Johan M G

2002-12-01

I present an inventory of theories of war causation (and on the origin of war) in preindustrial (traditional, foraging, 'primitive', hunter-gatherer, band- and tribe-level) societies, with emphasis on the roles of natural selection, sexual selection and kin selection. Also the school of sociocultural evolution is briefly discussed.

Ecological genetics of the Bromus tectorum (Poaceae) - Ustilago Bullata (Ustilaginaceae): A role for frequency dependent selection?

Treesearch

Susan E. Meyer; David L. Nelson; Suzette Clement; Alisa Ramakrishnan

2010-01-01

Evolutionary processes that maintain genetic diversity in plants are likely to include selection imposed by pathogens. Negative frequency-dependent selection is a mechanism for maintenance of resistance polymorphism in plant - pathogen interactions. We explored whether such selection operates in the Bromus tectorum - Ustilago bullata pathosystem. Gene-for-gene...

Fecundity selection on ornamental plumage colour differs between ages and sexes and varies over small spatial scales.

PubMed

Parker, T H; Wilkin, T A; Barr, I R; Sheldon, B C; Rowe, L; Griffith, S C

2011-07-01

Avian plumage colours are some of the most conspicuous sexual ornaments, and yet standardized selection gradients for plumage colour have rarely been quantified. We examined patterns of fecundity selection on plumage colour in blue tits (Cyanistes caeruleus L.). When not accounting for environmental heterogeneity, we detected relatively few cases of selection. We found significant disruptive selection on adult male crown colour and yearling female chest colour and marginally nonsignificant positive linear selection on adult female crown colour. We discovered no new significant selection gradients with canonical rotation of the matrix of nonlinear selection. Next, using a long-term data set, we identified territory-level environmental variables that predicted fecundity to determine whether these variables influenced patterns of plumage selection. The first of these variables, the density of oaks within 50 m of the nest, influenced selection gradients only for yearling males. The second variable, an inverse function of nesting density, interacted with a subset of plumage selection gradients for yearling males and adult females, although the strength and direction of selection did not vary predictably with population density across these analyses. Overall, fecundity selection on plumage colour in blue tits appeared rare and inconsistent among sexes and age classes. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

A single determinant dominates the rate of yeast protein evolution.

PubMed

Drummond, D Allan; Raval, Alpan; Wilke, Claus O

2006-02-01

A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we carry out the first combined analysis of seven predictors (gene expression level, dispensability, protein abundance, codon adaptation index, gene length, number of protein-protein interactions, and the gene's centrality in the interaction network) previously reported to have independent influences on protein evolutionary rates. Strikingly, our analysis reveals a single dominant variable linked to the number of translation events which explains 40-fold more variation in evolutionary rate than any other, suggesting that protein evolutionary rate has a single major determinant among the seven predictors. The dominant variable explains nearly half the variation in the rate of synonymous and protein evolution. We show that the two most commonly used methods to disentangle the determinants of evolutionary rate, partial correlation analysis and ordinary multivariate regression, produce misleading or spurious results when applied to noisy biological data. We overcome these difficulties by employing principal component regression, a multivariate regression of evolutionary rate against the principal components of the predictor variables. Our results support the hypothesis that translational selection governs the rate of synonymous and protein sequence evolution in yeast.

Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes.

PubMed

Toju, Hirokazu; Sota, Teiji

2009-09-01

One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio, likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae, the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.

Gene networks, occlusal clocks, and functional patches: new understanding of pattern and process in the evolution of the dentition.

PubMed

Polly, P David

2015-05-01

Our understanding of the evolution of the dentition has been transformed by advances in the developmental biology, genetics, and functional morphology of teeth, as well as the methods available for studying tooth form and function. The hierarchical complexity of dental developmental genetics combined with dynamic effects of cells and tissues during development allow for substantial, rapid, and potentially non-linear evolutionary changes. Studies of selection on tooth function in the wild and evolutionary functional comparisons both suggest that tooth function and adaptation to diets are the most important factors guiding the evolution of teeth, yet selection against random changes that produce malocclusions (selectional drift) may be an equally important factor in groups with tribosphenic dentitions. These advances are critically reviewed here.

Experimental evidence supports a sex-specific selective sieve in mitochondrial genome evolution.

PubMed

Innocenti, Paolo; Morrow, Edward H; Dowling, Damian K

2011-05-13

Mitochondria are maternally transmitted; hence, their genome can only make a direct and adaptive response to selection through females, whereas males represent an evolutionary dead end. In theory, this creates a sex-specific selective sieve, enabling deleterious mutations to accumulate in mitochondrial genomes if they exert male-specific effects. We tested this hypothesis, expressing five mitochondrial variants alongside a standard nuclear genome in Drosophila melanogaster, and found striking sexual asymmetry in patterns of nuclear gene expression. Mitochondrial polymorphism had few effects on nuclear gene expression in females but major effects in males, modifying nearly 10% of transcripts. These were mostly male-biased in expression, with enrichment hotspots in the testes and accessory glands. Our results suggest an evolutionary mechanism that results in mitochondrial genomes harboring male-specific mutation loads.

Selection on skewed characters and the paradox of stasis

PubMed Central

Bonamour, Suzanne; Teplitsky, Céline; Charmantier, Anne; Crochet, Pierre-André; Chevin, Luis-Miguel

2018-01-01

Observed phenotypic responses to selection in the wild often differ from predictions based on measurements of selection and genetic variance. An overlooked hypothesis to explain this paradox of stasis is that a skewed phenotypic distribution affects natural selection and evolution. We show through mathematical modelling that, when a trait selected for an optimum phenotype has a skewed distribution, directional selection is detected even at evolutionary equilibrium, where it causes no change in the mean phenotype. When environmental effects are skewed, Lande and Arnold’s (1983) directional gradient is in the direction opposite to the skew. In contrast, skewed breeding values can displace the mean phenotype from the optimum, causing directional selection in the direction of the skew. These effects can be partitioned out using alternative selection estimates based on average derivatives of individual relative fitness, or additive genetic covariances between relative fitness and trait (Robertson-Price identity). We assess the validity of these predictions using simulations of selection estimation under moderate samples size. Ecologically relevant traits may commonly have skewed distributions, as we here exemplify with avian laying date – repeatedly described as more evolutionarily stable than expected –, so this skewness should be accounted for when investigating evolutionary dynamics in the wild. PMID:28921508

Adaptive attunement of selective covert attention to evolutionary-relevant emotional visual scenes.

PubMed

Fernández-Martín, Andrés; Gutiérrez-García, Aída; Capafons, Juan; Calvo, Manuel G

2017-05-01

We investigated selective attention to emotional scenes in peripheral vision, as a function of adaptive relevance of scene affective content for male and female observers. Pairs of emotional-neutral images appeared peripherally-with perceptual stimulus differences controlled-while viewers were fixating on a different stimulus in central vision. Early selective orienting was assessed by the probability of directing the first fixation towards either scene, and the time until first fixation. Emotional scenes selectively captured covert attention even when they were task-irrelevant, thus revealing involuntary, automatic processing. Sex of observers and specific emotional scene content (e.g., male-to-female-aggression, families and babies, etc.) interactively modulated covert attention, depending on adaptive priorities and goals for each sex, both for pleasant and unpleasant content. The attentional system exhibits domain-specific and sex-specific biases and attunements, probably rooted in evolutionary pressures to enhance reproductive and protective success. Emotional cues selectively capture covert attention based on their bio-social significance. Copyright © 2017 Elsevier Inc. All rights reserved.

Behavioral and neural Darwinism: selectionist function and mechanism in adaptive behavior dynamics.

PubMed

McDowell, J J

2010-05-01

An evolutionary theory of behavior dynamics and a theory of neuronal group selection share a common selectionist framework. The theory of behavior dynamics instantiates abstractly the idea that behavior is selected by its consequences. It implements Darwinian principles of selection, reproduction, and mutation to generate adaptive behavior in virtual organisms. The behavior generated by the theory has been shown to be quantitatively indistinguishable from that of live organisms. The theory of neuronal group selection suggests a mechanism whereby the abstract principles of the evolutionary theory may be implemented in the nervous systems of biological organisms. According to this theory, groups of neurons subserving behavior may be selected by synaptic modifications that occur when the consequences of behavior activate value systems in the brain. Together, these theories constitute a framework for a comprehensive account of adaptive behavior that extends from brain function to the behavior of whole organisms in quantitative detail. Copyright (c) 2009 Elsevier B.V. All rights reserved.