scholarly journals Testing the neutral hypothesis of phenotypic evolution

2016 ◽  
Author(s):  
Wei-Chin Ho ◽  
Yoshikazu Ohya ◽  
Jianzhi Zhang
Keyword(s):  
Morphological Traits ◽  
Genomic Sequence ◽  
Morphological Evolution ◽  
Large Fraction ◽  
Neutral Theory ◽  
Phenotypic Evolution ◽  
Sequence Variations ◽  
Genomic Studies ◽  
The One ◽  
Multiple Strains

It is generally accepted that a large fraction of genomic sequence variations within and between species are neutral or nearly so1. Whether the same is true for phenotypic variations is a central question in biology2-7. On the one hand, numerous phenotypic adaptations have been documented2,8,9 and even Kimura, the champion of the neutral theory of molecular evolution, believed in widespread adaptive phenotypic evolution1. On the other hand, phenotypic studies are strongly biased toward traits that are likely to be adaptive9, contrasting genomic studies that are typically unbiased. It is thus desirable to test the neutral hypothesis of phenotypic evolution using traits irrespective of their potential involvement in adaptation. Here we present such a test for 210 morphological traits measured in multiple strains of the yeast Saccharomyces cerevisiae and two related species. Our test is based on the premise that, under neutrality, the rate of phenotypic evolution declines as the trait becomes more important to fitness, analogous to the neutral paradigm that functional genes evolve more slowly than functionless pseudogenes10. Neutrality is rejected in favor of adaptation if important traits evolve faster than less important ones, parallel to the demonstration of molecular adaptation when a functional gene evolves faster than pseudogenes. After controlling for the mutational size, we find faster evolution of more important morphological traits within and between species. By contrast, an analysis of 3466 yeast gene expression traits fails to reject neutrality. Thus, yeast morphological evolution is largely adaptive, but the same may not apply to other classes of phenotypes.

scholarly journals Testing the neutral hypothesis of phenotypic evolution

2017 ◽  
Vol 114 (46) ◽  
pp. 12219-12224 ◽  
Author(s):  
Wei-Chin Ho ◽  
Yoshikazu Ohya ◽  
Jianzhi Zhang
Keyword(s):  
Morphological Traits ◽  
Genetic Model ◽  
Morphological Evolution ◽  
Model Organisms ◽  
Functional Genes ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Important Principle ◽  
Phenotypic Variations ◽  
Evolution By Natural Selection

Although evolution by natural selection is widely regarded as the most important principle of biology, it is unknown whether phenotypic variations within and between species are mostly adaptive or neutral due to the lack of relevant studies of large, unbiased samples of phenotypic traits. Here, we examine 210 yeast morphological traits chosen because of experimental feasibility irrespective of their potential adaptive values. Our analysis is based on the premise that, under neutrality, the rate of phenotypic evolution measured in the unit of mutational size declines as the trait becomes more important to fitness, analogous to the neutral paradigm that functional genes evolve more slowly than functionless pseudogenes. However, we find faster evolution of more important morphological traits within and between species, rejecting the neutral hypothesis. By contrast, an analysis of 3,466 gene expression traits fails to refute neutrality. Thus, at least in yeast, morphological evolution appears largely adaptive, but the same may not apply to other classes of phenotypes. Our neutrality test is applicable to other species, especially genetic model organisms, for which estimations of mutational size and trait importance are relatively straightforward.

scholarly journals Biomechanical trade-offs bias rates of evolution in the feeding apparatus of fishes

2011 ◽  
Vol 279 (1732) ◽  
pp. 1287-1292 ◽  
Author(s):  
Roi Holzman ◽  
David C. Collar ◽  
Samantha A. Price ◽  
C. Darrin Hulsey ◽  
Robert C. Thomson ◽  
...  
Keyword(s):  
Genetic Factors ◽  
Morphological Evolution ◽  
The Body ◽  
Body Parts ◽  
Phenotypic Evolution ◽  
Genetic Constraints ◽  
Functional Systems ◽  
Rates Of Evolution ◽  
Trade Offs

Morphological diversification does not proceed evenly across the organism. Some body parts tend to evolve at higher rates than others, and these rate biases are often attributed to sexual and natural selection or to genetic constraints. We hypothesized that variation in the rates of morphological evolution among body parts could also be related to the performance consequences of the functional systems that make up the body. Specifically, we tested the widely held expectation that the rate of evolution for a trait is negatively correlated with the strength of biomechanical trade-offs to which it is exposed. We quantified the magnitude of trade-offs acting on the morphological components of three feeding-related functional systems in four radiations of teleost fishes. After accounting for differences in the rates of morphological evolution between radiations, we found that traits that contribute more to performance trade-offs tend to evolve more rapidly, contrary to the prediction. While ecological and genetic factors are known to have strong effects on rates of phenotypic evolution, this study highlights the role of the biomechanical architecture of functional systems in biasing the rates and direction of trait evolution.

scholarly journals The commonness of rarity: Global and future distribution of rarity across land plants

2019 ◽  
Author(s):  
Brian Joseph Enquist ◽  
Xiao Feng ◽  
Bradley Boyle ◽  
Brian Maitner ◽  
Erica A. Newman ◽  
...  
Keyword(s):  
Plant Species ◽  
Rare Species ◽  
Large Fraction ◽  
Neutral Theory ◽  
Species Abundance ◽  
Land Plant ◽  
Observation Data ◽  
Heavy Tailed Distributions ◽  
Species Abundance Distributions ◽  
Heavy Tailed

A key feature of life’s diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant species observation data in order to quantify the fraction of Earth’s extant land plant biodiversity that is common versus rare. Tests of different hypotheses for the origin of species commonness and rarity indicates that sampling biases and prominent models such as niche theory and neutral theory cannot account for the observed prevalence of rare species. Instead, the distribution of commonness is best approximated by heavy-tailed distributions like the Pareto or Poisson-lognormal distributions. As a result, a large fraction, ~36.5% of an estimated ~435k total plant species, are exceedingly rare. We also show that rare species tend to cluster in a small number of ‘hotspots’ mainly characterized by being in tropical and subtropical mountains and areas that have experienced greater climate stability. Our results indicate that (i) non-neutral processes, likely associated with reduced risk of extinction, have maintained a large fraction of Earth’s plant species but that (ii) climate change and human impact appear to now and will disproportionately impact rare species. Together, these results point to a large fraction of Earth’s plant species are faced with increased chances of extinction. Our results indicate that global species abundance distributions have important implications for conservation planning in this era of rapid global change.

scholarly journals Intra- and inter-specific variations of gene expression levels in yeast are largely neutral

2016 ◽  
Author(s):  
Jian-Rong Yang ◽  
Calum Maclean ◽  
Chungoo Park ◽  
Huabin Zhao ◽  
Jianzhi Zhang
Keyword(s):  
Gene Expression ◽  
Genome Sequence ◽  
Large Fraction ◽  
General Role ◽  
Expression Levels ◽  
Genome Wide ◽  
Sequence Variations ◽  
Expression Evolution ◽  
Molecular Phenotypes ◽  
Gene Expression Levels

ABSTRACTIt is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments. We find that the transcriptome-based clustering of the nine strains approximates the genome sequence-based phylogeny irrespective of their ecological environments. Remarkably, only ∼0.5% of genes exhibit similar expression levels among strains from a common ecological environment, no greater than that among strains with comparable phylogenetic relationships but different environments. These and other observations strongly suggest that most intra- and inter-specific variations in yeast gene expression levels result from the accumulation of random mutations rather than environmental adaptations. This finding has profound implications for understanding the driving force of gene expression evolution, genetic basis of phenotypic adaptation, and general role of stochasticity in evolution.

Phytoseiidae mites associated with native and cultivated solanaceous in Central-West Brazil

2021 ◽  
Author(s):  
Mércia Elias Duarte ◽  
Peterson Rodrigo Demite ◽  
Renata Santos De Mendonça ◽  
Miguel Michereff-filho ◽  
Maria Luiza Santa Cruz De Mesquita Alves ◽  
...  
Keyword(s):  
Biological Control ◽  
Morphological Traits ◽  
Common Species ◽  
Predatory Mites ◽  
Natural Environments ◽  
Phytoseiid Mites ◽  
Control Programs ◽  
Phytophagous Mites ◽  
Wild Host ◽  
The One

Predatory mites represent important biological control agents and those belonging to the Phytoseiidae family are the most promising for the control of phytophagous mites and small insects. The control of key pests of tomato and other solanaceous crops, highlighting phytophagous mites, has been a challenge and the biological control constitutes a promising strategy. Prospecting predatory mites in wild host plants, natural environments as well as in agroecosystems is relevant because these non-crop and crop areas can serve as reservoirs for promising species for biological control programs. This study aimed to know the Phytoseiidae fauna associated with wild and cultivated solanaceous plants in a poorly prospected area in Brazil, the Central-West Region. A detailed taxonomic identification of phytoseiid mites was conducted, and the most important morphological traits are presented for each species. In addition, associated phytophagous mites mainly belonging to the Tetranychidae, Tenuipalpidae and Eriophyoidea were identified. Surveys were carried out in 23 species of solanaceous collected in the Distrito Federal (12 areas) and Goiás State (1 area), from February 2017 to January 2018. Nineteen species of predators belonging to ten genera were recorded: Amblyseius (2 species), Euseius (3), Galendromus (1), Iphiseiodes (1), Neoseiulus (3), Paraphytoseius (1), Phytoseius (3), Proprioseiopsis (2), Typhlodromalus (2, one probably new to science) and Typhlodromips (1). Solanum lycocarpum was the solanaceous that harbored the highest richness (11 species), as well as the one with the highest abundance of phytoseiids (250 specimens). Typhlodromalus aripo was the most common species, being the most abundant (423 specimens; 32%) and registered on the largest number of hosts (14). Many of phytoseiid species found present morphological traits that facilitate their occurrence in leaves with trichomes, as in the case of tomato and other cultivated solanaceous. These traits and the association between predators and phytophagous mites may indicate that these species are promising for biological control programms. Thus, extensive studies to assess the efficiency of the identified predatory mites to control key solanaceous pests are required.

The Intellectual Challenge of Morphological Evolution: A Case for Variational Structuralism

2014 ◽  
Author(s):  
Günter P. Wagner
Keyword(s):  
Developmental Biology ◽  
Evolutionary Biology ◽  
Morphological Evolution ◽  
Evolutionary Developmental Biology ◽  
Phenotypic Evolution ◽  
Developmental Variation ◽  
Core Idea ◽  
Intellectual Challenge

This chapter explores variational structuralism, whose core idea is that organisms and their parts play causal roles in shaping the patterns of phenotypic evolution. Drawing on the work of pioneers such as Ron Amundson, it discusses the conceptual incompatibilities between two styles of thinking in evolutionary biology: functionalism and structuralism. It proceeds by explaining the meaning of developmental types and structuralist concepts arising from macromolecular studies. It also examines facts and ideas about bodies, Rupert Riedl's theory of the “immitatory epigenotype,” and Neil Shubin and Pere Alberch's developmental interpretation of tetrapod limbs. Finally, it looks at the emergence of molecular structuralism and the enigma of developmental variation. The chapter argues that typology naturally emerged from the facts of evolutionary developmental biology and that it would be seriously problematic to try to avoid it.

scholarly journals The commonness of rarity: Global and future distribution of rarity across land plants

2019 ◽  
Vol 5 (11) ◽  
pp. eaaz0414 ◽  
Author(s):  
Brian J. Enquist ◽  
Xiao Feng ◽  
Brad Boyle ◽  
Brian Maitner ◽  
Erica A. Newman ◽  
...  
Keyword(s):  
Plant Species ◽  
Conservation Planning ◽  
Rare Species ◽  
Extinction Risk ◽  
Large Fraction ◽  
Neutral Theory ◽  
Species Abundance ◽  
Risk Assessments ◽  
Human Land Use ◽  
Species Abundance Distributions

A key feature of life’s diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth’s plant biodiversity that are rare. A large fraction, ~36.5% of Earth’s ~435,000 plant species, are exceedingly rare. Sampling biases and prominent models, such as neutral theory and the k-niche model, cannot account for the observed prevalence of rarity. Our results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth’s plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species. Estimates of global species abundance distributions have important implications for risk assessments and conservation planning in this era of rapid global change.

scholarly journals Geographic variation in the morphology of the sand-dwelling lizard Nothobachia ablephara (Squamata: Gymnophthalmidae)

2019 ◽  
Vol 18 (2) ◽  
pp. 195-207
Author(s):  
Carolina Nisa Ramiro ◽  
Renato Sousa Recoder ◽  
Miguel Trefaut Rodrigues
Keyword(s):  
Geographic Variation ◽  
Morphological Traits ◽  
Geographical Variation ◽  
Multivariate Analyses ◽  
Molecular Study ◽  
Northeastern Brazil ◽  
Sexually Dimorphic ◽  
Morphometric Variation ◽  
The One ◽  
Two Populations

Geographic variation in the morphology of the sand-dwelling lizard Nothobachia ablephara (Squamata: Gymnophthalmidae). Nothobachia ablephara is a small microteiid lizard with an elongated body and reduced limbs; it occurs in isolated dune felds in the state of Bahia (Xique-Xique and Alagoado) and small sandy patches in northeastern Brazil. A previous molecular study found a marked mtDNA divergence between populations of N. ablephara from Alagoado and Xique-Xique dunes, suggesting that the two populations diverged from one another between 3 and 4 million years ago. Given this isolation, it is interesting to explore whether morphological traits of the lizards refect the reported genetic divergence of the populations. Scale counts of the sexes and the populations differ signifcantly, but there is considerable overlap of values. Univariate and multivariate analyses revealed signifcant morphometric variation between sexes and populations; however, this is mostly explained by size differences. Females are larger than males in all characters that are sexually dimorphic, and individuals from Xique-Xique are larger than those from Alagoado in all characters that vary geographically. The sample from Alagoado has more sexually dimorphic characters than the one from Xique-Xique. Although N. ablephara displays some geographical variation, the two populations could not be unequivocally distinguished by scale counts and morphometric data.

scholarly journals Three-dimensional maps of interstellar dust in the Local Arm: using Gaia, 2MASS, and APOGEE-DR14

2018 ◽  
Vol 616 ◽  
pp. A132 ◽  
Author(s):  
R. Lallement ◽  
L. Capitanio ◽  
L. Ruiz-Dern ◽  
C. Danielski ◽  
C. Babusiaux ◽  
...  
Keyword(s):  
Interstellar Dust ◽  
Large Scale ◽  
Galactic Plane ◽  
Large Fraction ◽  
Complex Structure ◽  
Dust Emission ◽  
Three Dimensional ◽  
Red Giants ◽  
Photometric Calibration ◽  
The One

Context. Gaia data and stellar surveys open the way to the construction of detailed 3D maps of the Galactic interstellar (IS) dust based on the synthesis of star distances and extinctions. Dust maps are tools of broad use, also for Gaia-related Milky Way studies. Aims. Reliable extinction measurements require very accurate photometric calibrations. We show the first step of an iterative process linking 3D dust maps and photometric calibrations, and improving them simultaneously. Methods. Our previous 3D map of nearby IS dust was used to select low-reddening SDSS/APOGEE-DR14 red giants, and this database served for an empirical effective temperature- and metallicity-dependent photometric calibration in the Gaia G and 2MASS Ks bands. This calibration has been combined with Gaia G-band empirical extinction coefficients recently published, G, J, and Ks photometry and APOGEE atmospheric parameters to derive the extinction of a large fraction of the survey targets. Distances were estimated independently using isochrones and the magnitude-independent extinction KJ−Ks. This new dataset has been merged with the one used for the earlier version of dust map. A new Bayesian inversion of distance-extinction pairs has been performed to produce an updated 3D map. Results. We present several properties of the new map. A comparison with 2D dust emission reveals that all large dust shells seen in emission at middle and high latitudes are closer than 300 pc. The updated distribution constrains the well-debated, X-ray bright North Polar Spur to originate beyond 800 pc. We use the Orion region to illustrate additional details and distant clouds. On the large scale the map reveals a complex structure of the Local Arm. Chains of clouds of 2–3 kpc in length appear in planes tilted by ≃15° with respect to the Galactic plane. A series of cavities oriented along a l ≃ 60–240° axis crosses the Arm. Conclusions. The results illustrate the ongoing synergy between 3D mapping of IS dust and stellar calibrations in the context of Gaia. Dust maps provide prior foregrounds for future calibrations appropriate to different target characteristics or ranges of extinction, allowing us in turn to increase extinction data and produce more detailed and extended maps.

scholarly journals Recent Results from the Antares Neutrino Telescope

2019 ◽  
Vol 207 ◽  
pp. 01001
Author(s):  
Antoine Kouchner
Keyword(s):  
Galactic Plane ◽  
Large Fraction ◽  
Neutrino Flux ◽  
High Energy ◽  
Neutrino Telescope ◽  
Point Sources ◽  
Joint Analysis ◽  
Neutrino Source ◽  
Cosmic Neutrino ◽  
The One

Antares, the first undersea neutrino telescope, has been continuously operating since 2007 in the Mediterranean Sea. The transparency of the water allows for a very good angular resolution in the reconstruction of neutrino events of all flavors. This results in an unmatched sensitivity for neutrino source searches, in a large fraction of the Southern Sky, at TeV energies. As a consequence, Antares provides valuable constraints on the origin of the cosmic neutrino flux discovered by the IceCube Collaboration. Based on an all-flavor dataset spanning nine years of operation of the detector, the latest results of Antares searches for neutrino point sources, and for diffuse neutrino emission from the entire sky as well as from several interesting regions such as the Galactic Plane, are presented. Several results have been obtained through a joint analysis with the IceCube Collaboration. Concerning the multi-messenger program, the focus is made on the follow-up searches of IceCube alerts, in particular the one related to the TXS 0506+056 blazar, thought to be the first extragalactic high-energy neutrino source identified so far.

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