scholarly journals Thinking of Fish Population Discrimination: Population Average Phenotype vs. Population Phenotypes

2021 ◽  
Vol 8 ◽  
Author(s):  
Joana Vasconcelos ◽  
Alba Jurado-Ruzafa ◽  
José Luis Otero-Ferrer ◽  
Antoni Lombarte ◽  
Rodrigo Riera ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Phenotypic Diversity ◽  
Morphological Variability ◽  
Fish Population ◽  
Elliptic Fourier Analysis ◽  
Mainland Portugal ◽  
Population Discrimination ◽  
Population Average ◽  
Management Approaches ◽  
Parametric Algorithms

The genetic polymorphism and phenotypic variation are key in ecology and evolution. The morphological variability of the contour of fish otoliths has been extensively used for the delimitation of stocks. These studies are conventionally based on average phenotype using elliptic Fourier analysis and lineal discriminant analysis as classifier. Considering new analytical options, such as the wavelet transform and non-parametric algorithms, we here analyzed the otolith shape of Trachurus picturatus (blue jack mackerel) from mainland Portugal, Madeira, and the Canaries. We explore the phenotypic variation throughout a latitudinal gradient, establish a hypothesis to explain this variability based on the reaction norms, and determine how the use of average phenotype and/or morphotypes influences in the delimitation of stocks. Four morphotypes were identified in all regions, with an increase of phenotypes in warmer waters. The findings demonstrated that stocks were clearly separated with classification rates over 90%. The use of morphotypes, revealed seasonal variations in their frequencies and per region. The presence of shared phenotypes in different proportions among fishing grounds may open new management approaches in migratory species. These results show the importance of the phenotypic diversity in fisheries management.

scholarly journals Phenotypic diversity and plasticity index of Eurycoma apiculata populations in Eastern Sumatra, Indonesia based on leaves morphology

2020 ◽  
Vol 21 (7) ◽  
Author(s):  
Zulfahmi Zulfahmi ◽  
Edi Purwanto ◽  
Parjanto ◽  
Ahmad Yunus
Keyword(s):  
Phenotypic Plasticity ◽  
Phenotypic Variation ◽  
Phenotypic Diversity ◽  
In Situ Conservation ◽  
Plasticity Index ◽  
Ex Situ ◽  
Phenotypic Traits ◽  
Phenotypic Differentiation ◽  
Riau Archipelago ◽  
Conservation Method

Abstract. Zulfahmi, Purwanto E, Parjanto, Yunus A. 2020. Phenotypic diversity and plasticity index of Eurycoma apiculata populations in Eastern Sumatra, Indonesia based on leaves morphology. Biodiversitas 21: 2923-2934. Eurycoma apiculata A.W. Benn. is a protected species in Indonesia, but diversity information of this species is limited. The objective of this study was to assess the phenotypic diversity, phenotypic plasticity index, and phenotypic differentiation among populations of E. apiculata in Eastern Sumatra, Indonesia based on leaves morphology. A total of 45 traits were measured on leaves from six populations studied. The result of this found that the phenotypic variation coefficient (CV) of the characters was ranged from 7.41% to 36.97%, revealed the abundant phenotypic variation in the species. The phenotypic CV values of the population varied from 13.95% to 24.10%. The CV values of all populations from the mainland Sumatra (17.75%) were lower than that from the Riau archipelago (23.61%), which revealed that phenotypic traits in mainland Sumatra were more stable compared to populations in the Riau archipelago. The population phenotypic plasticity index value of populations ranged from 0.41 to 0.51, and it was classified as a moderate level. The phenotypic differentiation coefficient among populations in this study was relatively low (VST = 21.06%), indicating a lower phenotypic variation among populations than within populations. The scatter plot of principal component analysis and UPGMA dendrogram divided the six populations studies into two groups. The findings of this study recommend that the in-situ conservation method is an effective protection strategy for E. apiculata while ex-situ conservation method can be implemented as a supplementary method.

scholarly journals On the Use of Blood Samples for Measuring DNA Methylation in Ecological Epigenetic Studies

2020 ◽  
Vol 60 (6) ◽  
pp. 1558-1566 ◽  
Author(s):  
Arild Husby
Keyword(s):  
Dna Methylation ◽  
Phenotypic Variation ◽  
Evolutionary Biology ◽  
Phenotypic Diversity ◽  
Genomic Region ◽  
Epigenetic Mechanism ◽  
Blood Samples ◽  
Reduced Representation ◽  
Bisulfite Treatment ◽  
Methylation Patterns

Synopsis There is increasing interest in understanding the potential for epigenetic factors to contribute to phenotypic diversity in evolutionary biology. One well studied epigenetic mechanism is DNA methylation, the addition of a methyl group to cytosines, which have the potential to alter gene expression depending on the genomic region in which it takes place. Obtaining information about DNA methylation at genome-wide scale has become straightforward with the use of bisulfite treatment in combination with reduced representation or whole-genome sequencing. While it is well recognized that methylation is tissue specific, a frequent limitation for many studies is that sampling-specific tissues may require sacrificing individuals, something which is generally undesirable and sometimes impossible. Instead, information about DNA methylation patterns in the blood is frequently used as a proxy tissue. This can obviously be problematic if methylation patterns in the blood do not reflect that in the relevant tissue. Understanding how, or if, DNA methylation in blood reflect DNA methylation patterns in other tissues is therefore of utmost importance if we are to make inferences about how observed differences in methylation or temporal changes in methylation can contribute to phenotypic variation. The aim of this review is to examine what we know about the potential for using blood samples in ecological epigenetic studies. I briefly outline some methods by which we can measure DNA methylation before I examine studies that have compared DNA methylation patterns across different tissues and, finally, examine how useful blood samples may be for ecological studies of DNA methylation. Ecological epigenetic studies are in their infancy, but it is paramount for the field to move forward to have detailed information about tissue and time dependence relationships in methylation to gain insights into if blood DNA methylation patterns can be a reliable bioindicator for changes in methylation that generate phenotypic variation in ecologically important traits.

Genomic evolution of the marine bacterium Phaeobacter inhibens during biofilm growth

2021 ◽  
Author(s):  
Marwan E. Majzoub ◽  
Kerensa McElroy ◽  
Michael Maczka ◽  
Stefan Schulz ◽  
Torsten Thomas ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Phenotypic Variation ◽  
Phenotypic Diversity ◽  
Survival Strategies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Biofilm Growth ◽  
Tropodithietic Acid ◽  
Biofilm Dispersal ◽  
Phaeobacter Inhibens

P. inhibens 2.10 is an effective biofilm former on marine surfaces and has the ability to outcompete other microorganisms, possibly due to the production of the plasmid-encoded, secondary metabolite tropodithietic acid (TDA). P. inhibens 2.10 biofilms produce phenotypic variants with reduced competitiveness compared to the wild-type. In the present study, we used longitudinal, genome-wide deep sequencing to uncover the genetic foundation that contributes to the emergent phenotypic diversity in P. inhibens 2.10 biofilm dispersants. Our results show that phenotypic variation is not due to the loss of plasmid that encodes the genes for the TDA synthesis, but instead show that P. inhibens 2.10 biofilm populations become rapidly enriched in single nucleotide variations in genes involved in the synthesis of TDA. While variants in genes previously linked to other phenotypes, such as lipopolysaccharide production (i.e. rfbA ) and celluar persistence (i.e. metG ), also appear to be selected for during biofilm dispersal, the number and consistency of variations found for genes involved in TDA production suggest that this metabolite imposes a burden for P. inhibens 2.10 cells. Our results indicate a strong selection pressure for the loss of TDA in mono-species biofilm populations and provide insight into how competition (or lack thereof) in biofilms might shape genome evolution in bacteria. Importance Statement Biofilm formation and dispersal are important survival strategies for environmental bacteria. During biofilm dispersal cells often display stable and heritable variants from the parental biofilm. Phaeobacter inhibens is an effective colonizer of marine surfaces, in which a subpopulation of its biofilm dispersal cells displays a non-competitive phenotype. This study aimed to elucidate the genetic basis of these phenotypic changes. Despite the progress made to date in characterizing the dispersal variants in P. inhibens , little is understood about the underlying genetic changes that result in the development of the specific variants. Here, P. inhibens phenotypic variation was linked to single nucleotide polymorphisms (SNPs), in particular in genes affecting the competitive ability of P. inhibens , including genes related to the production of the antibiotic tropodithietic acid (TDA) and bacterial cell-cell communication (e.g. quorum sensing). This work is significant as it reveals how the biofilm-lifestyle might shape genome evolution in a cosmopolitan bacterium.

scholarly journals Biodiversity Evaluation of Geotrichum candidum Link. Is Arthrosporic Nucleus Number in Geotrichum candidum related to the Fungus Biodiversity?

2016 ◽  
Vol 47 (4) ◽  
pp. 181-186
Author(s):  
M. Koňuchová ◽  
V. Lehotová ◽  
A. Šípková ◽  
E. Piecková ◽  
Ľ. Valík
Keyword(s):  
Phenotypic Diversity ◽  
Morphological Variability ◽  
Geotrichum Candidum ◽  
Microscopic Structure ◽  
Hoechst 33258 ◽  
Microscopic Fungus

Abstract Geotrichum candidum species exhibits properties of both moulds and yeasts and its affiliation to one of the groups has been intensively discussed. It is because this filamentous microscopic fungus is displaying substantial morphological variability and wide phenotypic diversity. The present study assesses the variability of arthrosporic nucleus number of twelve isolates of G. candidum originating from artisanal manufacturing and ripened traditional Slovak cheeses. Results showed that arthrospores of the studied isolates contained on average 1.5 ± 0.7 (on the Gorodkova medium) and 1.5 ± 0.6 (on the McClary medium) Hoechst 33258-stained nuclei (range 1–4 nuclei on both agars) after a 7-day cultivation at 25°C. Majority of arthrospores comprised one nucleus, irrespective to the used nutrient-limited medium. Generally, a higher relative nucleus number per arthrospore was exhibited in yeast-like isolates with microscopic structure composed predominantly of spores, while it was lower in vegetative hyphae. These isolates originated from ewe’s lump cheese. Our study reveals that the arthrosporic nucleus number of the G. candidum strains is closely related to morphotype and origin of this yeast.

Morphometric Methods for Applied Ostracodology: Tools for Outline Analysis of Nonmarine Ostracodes

2003 ◽  
Vol 9 ◽  
pp. 101-118 ◽  
Author(s):  
Angel Baltanás ◽  
Wolfgang Brauneis ◽  
Dan L. Danielopol ◽  
Johann Linhart
Keyword(s):  
Shape Change ◽  
Morphological Variability ◽  
Geographic Distance ◽  
Morphological Diversity ◽  
Population Level ◽  
Procrustes Analysis ◽  
Elliptic Fourier Analysis ◽  
Mathematical Basis ◽  
B Splines ◽  
Morphometric Methods

Morphometric techniques for the analysis of shape change in organisms have experienced a noteworthy development in the last decade. But despite the significant contributions that ostracodologists made to the field, their use in standard ostracode research is far from common. This contribution stresses the usefulness of morphometric methods to describe ostracode valve outlines and to summarize shape changes cued by environmental factors. Focus is on nonmarine ostracodes which are generally poorly ornamented so that their carapaces offer few landmarks for characterization of morphological change. Out of several alternatives three techniques for shape analysis are applied here: the B-splines method for approximative description of ostracode contours, Elliptic Fourier Analysis (EFA) and a Generalized (Resistant Fit) Procrustes Analysis. B-splines method is presented here for the first time within a biological framework and both its mathematical basis and practical usage are discussed. Additionally a computer program, Morphomatica, developed for performing B-splines analyses of ostracod outlines is briefly documented.Three case studies exemplify here how morphometric analysis might help either to detect environmental influences in ostracode shape or to show how morphological diversity of ostracode valve reflects environmental change. First, morphological variability within a clonal lineage of Heterocypris barbara (Gauthier and Brehm) is shown to be related to environmental variables (mainly temperature) when raised under controlled conditions in the lab. Second, carapace variability at the population level is explored in a widely distributed species (Limnocythere inopinata Baird) sampled from distant localities. Morphometric analyses illustrate how such variability is not related to geographic distance but to environmental conditions. Finally, patterns of temporal change in morphological diversity of a widely distributed ostracode group, the Candoninae, are elucidated by using the B-splines method combined with multivariate statistical analysis.It is concluded that morphometric methods deserve to be included in the methodological toolbox of practicing ostracodologists as they can provide useful information in ecological and paleoecological research.

Morphological and molecular diversity and genetic structure of Moroccan cultivated almond (Prunus dulcisMill.) beside some foreign varieties

2014 ◽  
Vol 12 (3) ◽  
pp. 308-316 ◽  
Author(s):  
Abdelali El Hamzaoui ◽  
Ahmed Oukabli ◽  
Mohiéddine Moumni
Keyword(s):  
Morphological Traits ◽  
Phenotypic Diversity ◽  
Morphological Variability ◽  
Principal Component ◽  
Leaf Traits ◽  
Prunus Dulcis ◽  
Fruit Traits ◽  
Plant Materials ◽  
Breeding Programmes ◽  
Clustering Approach

In this study, 15 morphological traits and 16 microsatellite markers were used to assess the morphological variability and structure of 68 (33 local and 35 foreign) almond accessions (Prunus dulcis(Mill.) D.A. Webb). Extensive phenotypic diversity was found among the accessions, and results indicated a high variation in leaf and fruit traits. Varieties were separated into two distinct groups with a similarity coefficient of 0.761. Morphological traits were categorized by principal component analysis into five components, which explained 86.5% of the total variation. Nut and kernel traits were dominant in the two first components, accounting for 49.4% of the variation. By contrast, leaf traits accounted for 18.4% of the variation in the third component. The results of molecular analysis (Bayesian clustering approach) did not correspond to morphological groupings, and the second approach was more discriminate. The combination of both approaches revealed the richness among the collected plant materials, which will be useful in breeding programmes of this species.

scholarly journals Phenotypic Diversity of Doum Palm (Hyphaene compressa), a Semi‐Domesticated Palm in the Arid and Semi‐Arid Regions of Kenya

Scientifica ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Agnes Omire ◽  
Nancy L. M. Budambula ◽  
Johnstone Neondo ◽  
Robert Gituru ◽  
Cecilia Mweu
Keyword(s):  
Rural Communities ◽  
Morphological Traits ◽  
Phenotypic Diversity ◽  
Morphological Variability ◽  
Coastal Region ◽  
Principal Component ◽  
Morphological Characters ◽  
Fruit Traits ◽  
Coastal Regions ◽  
Linear Discriminant

Hyphaene compressa is an economically important palm in Africa. Despite its significant role in the livelihoods of rural communities, the diversity of doum palm is poorly documented and studied. In addition, it has no model descriptor that can aid such studies. Ninety H. compressa accessions collected from Northern, Eastern, and Coastal regions of Kenya were examined to determine the morphological variability of the vegetative and fruit traits of H. compressa and to identify its morphotypes for improvement. A total of 19 morphological characters including seven quantitative and 12 qualitative traits of fruit and vegetative traits were selected. Linear mixed-effects models, principal component analysis, and linear discriminant analyses were used to assess the variation in the morphological traits of doum palm based on the regions. Hierarchical clustering was performed to identify the morphotypes of H. compressa. There was variability in H. compressa morphological traits, particularly at the Kenyan Coast. All seven quantitative traits were able to effectively discriminate doum palm phenotypically p ≤ 0.001 . The 90 accessions clustered into five morphotypes designated as 1, 2, 3, 4, and 5. Morphotype 4 was specific only to the Coastal region. Morphotype 5 had the tallest trees with the biggest fruits and included palms from Eastern and Coastal regions making it the best morphotype for fruit traits. This study will inform the domestication, improvement, and conservation of H. compressa by selecting elite accessions.

scholarly journals Exploring the functional meaning of head shape disparity in aquatic snakes

2020 ◽  
Author(s):  
Marion Segall ◽  
Raphaël Cornette ◽  
Ramiro Godoy-Diana ◽  
Anthony Herrel
Keyword(s):  
Phenotypic Diversity ◽  
Morphological Variability ◽  
Shape Variation ◽  
Head Shape ◽  
Diet Specialization ◽  
Selective Pressures ◽  
Niche Specialization ◽  
3D Printed ◽  
Selection For ◽  
Selective Regime

AbstractPhenotypic diversity, or disparity, can be explained by simple genetic drift or, if functional constraints are strong, by selection for ecologically relevant phenotypes. We here studied phenotypic disparity in head shape in aquatic snakes. We investigated whether conflicting selective pressures related to different functions have driven shape diversity and explore whether similar phenotypes may give rise to the same functional output (i.e. many-to-one mapping of form to function). We focused on the head shape of aquatically foraging snakes as they fulfil several fitness-relevant functions and show a large amount of morphological variability. We used 3D surface scanning and 3D geometric-morphometrics to compare the head shape of 62 species in a phylogenetic context. We first tested whether diet specialization and size are drivers of head shape diversification. Next, we tested for many-to-one mapping by comparing the hydrodynamic efficiency of head shapes characteristic of the main axis of variation in the dataset. We 3D printed these shapes and measured the forces at play during a frontal strike. Our results show that diet and size explain only a small amount of shape variation. Shapes did not functionally converge as more specialized aquatic species evolved a more efficient head shape than others. The shape disparity observed could thus reflect a process of niche specialization under a stabilizing selective regime.

scholarly journals Assessment of phenotypic variability among EEA INTA Pergamino sunflower lines: Its relationship with the grain yield and oil content

OCL ◽  
2021 ◽  
Vol 28 ◽  
pp. 33
Author(s):  
Matías Domínguez ◽  
Stefanía Herrera ◽  
Julio Horacio González
Keyword(s):  
Grain Yield ◽  
Oil Content ◽  
Phenotypic Diversity ◽  
Phenotypic Variability ◽  
Morphological Variability ◽  
Principal Component ◽  
Hierarchical Cluster ◽  
Breeding Program ◽  
Depth Study ◽  
Selective Forces

The aims of the present study were to assess the phenotypic diversity among 221 sunflower accessions of INTA Pergamino Sunflower Breeding Program, to obtain discriminant functions that allow the classification of new accessions in similar groups and to evaluate the relationship between genetic distance pairwise accessions and hybrid performance for grain yield and oil content. We used 19 quantitative descriptors to evaluate phenotypic and morphological variability. Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) were used to evaluate simultaneously all the variables and to describe phenotypic variation patterns of the germplasm. The distribution of germplasm in the dendrogram did not follow a clear pattern with regard to the predefined groups. This study revealed the variability observed among the lines that form the INTA Pergamino breeding program despite the highly selective forces applied to obtain inbred lines that produce superior hybrids for the Argentinean sunflower area. This work demonstrates the need for more in-depth study of genetic variability to be used as a predictor of heterosis in sunflower.

scholarly journals The tRNA-Tyr Gene Family ofSaccharomyces cerevisiae: Agents of Phenotypic Variation and Position Effects on Mutation Frequency

Genetics ◽  
2002 ◽  
Vol 161 (4) ◽  
pp. 1395-1410 ◽  
Author(s):  
Sayoko Ito-Harashima ◽  
Phillip E Hartzog ◽  
Himanshu Sinha ◽  
John H McCusker
Keyword(s):  
Gene Family ◽  
Phenotypic Variation ◽  
Mutation Frequency ◽  
Phenotypic Diversity ◽  
Position Effect ◽  
Low Frequency ◽  
Average Frequency ◽  
Very High Frequency ◽  
Position Effects ◽  
Tyr Gene

AbstractExtensive phenotypic diversity or variation exists in clonal populations of microorganisms and is thought to play a role in adaptation to novel environments. This phenotypic variation or instability, which occurs by multiple mechanisms, may be a form of cellular differentiation and a stochastic means for modulating gene expression. This work dissects a case of phenotypic variation in a clinically derived Saccharomyces cerevisiae strain involving a cox15 ochre mutation, which acts as a reporter. The ochre mutation reverts to sense at a low frequency while tRNA-Tyr ochre suppressors (SUP-o) arise at a very high frequency to produce this phenotypic variation. The SUP-o mutations are highly pleiotropic. In addition, although all SUP-o mutations within the eight-member tRNA-Tyr gene family suppress the ochre mutation reporter, there are considerable phenotypic differences among the different SUP-o mutants. Finally, and of particular interest, there is a strong position effect on mutation frequency within the eight-member tRNA-Tyr gene family, with one locus, SUP6, mutating at a much higher than average frequency and two other loci, SUP2 and SUP8, mutating at much lower than average frequencies. Mechanisms for the position effect on mutation frequency are evaluated.

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