Patterns Of Phenotypic Variation Research Articles

Multivariate Analysis of Genotype-Phenotype Association.

With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map has important consequences for gene identification and may shed light on the evolvability of organisms.

Relaxed predation results in reduced phenotypic integration in a suite of dragonflies.

Although changes in magnitude of single traits responding to selective agents have been studied intensively, little is known about selection shaping networks of traits and their patterns of covariation. However, this is central for our understanding of phenotypic evolution as traits are embedded in a multivariate environment with selection affecting a multitude of traits simultaneously rather than individually. Here, we investigate inter- and intraspecific patterns of trait integration (trait correlations) in the larval abdomen of dragonflies as a response to a change in predator selection. Species of the dragonfly genus Leucorrhinia underwent a larval habitat shift from predatory fish to predatory dragonfly-dominated lakes with an associated relaxation in selection pressure from fish predation. Our results indicate that the habitat-shift-induced relaxed selection pressure caused phenotypic integration of abdominal traits to be reduced. Intraspecific findings matched patterns comparing species from both habitats with higher abdominal integration in response to predatory fish. This higher integration is probably a result of faster burst swimming speed. The abdomen holds the necessary morphological machinery to successfully evade predatory fish via burst swimming. Hence, abdominal traits have to function in a tight coordinated manner, as maladaptive variation and consequently nonoptimal burst swimming would cause increased mortality. In predatory dragonfly-dominated lakes, no such strong link between burst swimming and mortality is present. Our findings highlight the importance of studying multivariate trait relationships as a response to selection for understanding patterns of phenotypic diversification.

Patterns of genetic and morphometric diversity in the marbled crab (Pachygrapsus marmoratus, Brachyura, Grapsidae) populations across the Tunisian coast

The present study reports on population structure analysis of the marbled crab Pachygrapsus marmoratus (Fabricius, 1787) from the Tunisian coast, an appropriate location to study biogeographical processes because of the presence of a well-known discontinuous biogeographic area (the Siculo-Tunisian Strait). Patterns of morphological and genetic variation of this highly dispersive and continuously distributed decapod species were assessed among its geographically close populations which cover almost the entire Tunisian coastline. A total of 386 specimens from nine sites were collected and examined for morphometric variability at 14 morphometric traits. The results of multivariate analyses of linear morphometric traits showed the existence of sexual dimorphism in this species by PERMANOVA (Permutational multivariate analysis of variance). In addition, both CDA (Canonical discriminant analysis) and NPMANOVA (Non parametric MANOVA test) analyses revealed statistically significant differences among the studied locations for both sexes. Overall, the outcome of CDA analysis showed that over 87% of individuals could be assigned correctly to three regional groups in both sexes (North, Center and South). Specifically, SIMPER (Similarity Percentages) analysis showed that carapace length, carapace width and merus length were major contributors to the morphometric separation between populations. The pattern of phenotypic variation suggested by morphometric analyses was found to be highly discordant with that suggested by the analysis of a mitochondrial marker (cytochrome oxidase I, COI). Indeed, the results inferred from restriction fragment analysis of the COI in 180 crabs, suggested high genetic homogeneity. Very low levels of haplotype diversity (h) were found in almost all the studied populations, associated with non significant genetic distances for nearly all population comparisons. Explanations to these morphometric and mtDNA patterns as well as the discrepancy between them are discussed.

Geographic variation of the sable (Martes zibellina L., 1758) within the range, and phylogeography

Analysis of skull size, fur color, and cranial phene FFCI has been performed in 57 sable population groups inhabiting the Russian part of the species range. Sample average character values have been matched to geographic coordinates, annual average air temperature, and elevation a.s.l. of the corresponding locality. Statistically significant correlations have been revealed, namely, direct correlations of skull size with geographic latitude and of fur color and FFCI phene with longitude and elevation a.s.l., and inverse correlations of this phene and fur color with temperature and latitude, and of skull size with longitude. The strength of these correlations in southern and northern populations of the species is different. As a rule, congruence is observed in the geographic variation of phenotypic characters: an increase in skull size is usually accompanied by statistically significant lightening of the fur color and decrease in FFCI phene frequency. Therefore, this regularity may be considered a species-specific feature. Supposedly, the observed pattern of phenotypic variation within the range represents the process of formation of the morphological appearance of populations in the course of postglacial radiation, i.e., reflects the phylogeography of the species.

Phenotypic Characterization on Selected Kenyan and Tanzanian Rice (Oryza sativa L) Populations Based on Grain Morphological Traits

Phenotypic characterization of rice varieties is a good approach for assessing genetic and phenotypic variability among varieties and is key in grading of rice varieties. The objective of this study was to determine the major determinants of phenotypic diversity and the strength of segregation among aromatic and non-aromatic rice (Oryza sativa L) populations collected from Kenya and Tanzania. Multivariate analyses including principal component analysis (PCA) and cluster analysis were carried out assess the overall patterns of morphological variation. Using Principal component analysis, it was found that grain length, kernel length, grain weight and kernel length/breadth ratio are major drivers of the huge phenotypic diversity observed. Cluster analysis was found to effectively distinguish the majority of aromatic from non-aromatic varieties based on the grain quality traits evaluated where two distinct clusters were formed. The results obtained from this study demonstrated that phenotypic trait measurement can be relied upon in diversity studies among diverse and closely related genotypes. We conclude that this research which forms first part of rice grading gives an insight in to the general patterns of phenotypic diversity and finds out the most important distinguishing characters. This will be validated with subsequent molecular analysis.

Diachronic Evidence in Nonmetric Morphological Characters of Teeth in Armenian Highland and Georgia Populations

The aim of the study is the assessment of biological distance between populations from Arme-nian highland and Georgia based on the frequency of nonmetric odontological traits. These traits are characterized by high inter-population differentiation, low sexual dimorphism, and relatively small intra and inter observer recordation error. This paper presents the results of the odontological differentiation of human populations from Armenian highland and Georgia. The comparative analysis was carried out on 12 populations. Trait frequencies for all populations were analysed using principal component analysis. Results support the following conclusions: The populations of Armenian highland and Georgia can be differentiated as far as the frequency of odontological traits are concerned. Biocultural diversity of ancient Transcaucasian populations has not been studied extensively, therefore delineating some of the patterns of phenotypic variation may be useful for understanding their ongoing evolution.

Multi-character approach reveals a discordant pattern of phenotypic variation during ontogeny in Culex pipiens biotypes (Diptera: Culicidae).

Culex (Culex) pipiens s.l. (Diptera: Culicidae) comprises two distinct biotypes, pipiens ('rural') and molestus ('urban'), both of which are thought to have differing capacities due to different host preferences. To better understand West Nile encephalitis epidemiology and improve risk assessment, local distinction between these forms is essential. This study assesses phenotypic variation at larval and adult stages of 'urban' and 'rural' biotypes of the species by complementary use of meristic, univariate and multivariate traits analyzed by traditional and geometric morphometrics. Third- and fourth-instar larvae from a broad area of the city of Novi Sad (Serbia) were collected and reared in the laboratory. After adult eclosion, the sex of each larva was recorded based on the sex of the corresponding adult. Examination of the association between variations of larval traits revealed contrasting variations regarding pecten spines vs. siphonal size and siphonal shape in the 'rural' biotype. Siphons of larvae collected in marshes and forest ecosystems outside urban areas were found to be the largest, but possessed the smallest number of pecten spines. In addition, statistically significant female-biased sexual dimorphism was observed in siphonal size, wing size and wing shape. Finally, we propose that an integrative approach is essential in delimitation of Cx. pipiens s.l. biotypes, since their differentiation was not possible based solely on larval and adult traits. Our findings shed light on the phenotypic plasticity important for population persistence in the changing environment of these medically important taxa.

Variation in wing pattern and palatability in a female-limited polymorphic mimicry system.

Checkerspot butterflies in the genera Euphydryas and Chlosyne exhibit phenotypic polymorphisms along a well-defined latitudinal and elevational gradient in California. The patterns of phenotypic variation in Euphydryas chalcedona, Chlosyne palla, and Chlosyne hoffmanni suggest a mimetic relationship; in addition, the specific patterns of variation in C. palla suggest a female-limited polymorphic mimicry system (FPM). However, the existence of polymorphic models runs counter to predictions of mimicry theory. Palatability trials were undertaken to assess whether or not the different color morphs of each species were distasteful or toxic to a generalized avian predator, the European starling (Sturnus vulgaris). Results indicate that the black morph of E. chalcedona is distasteful, but not toxic, to predators, while the red morph is palatable. C . hoffmanni and both color morphs of C. palla are palatable to predators. Predators that learn to reject black E. chalcedona also reject black C. palla, suggesting that the latter is a FPM of the former. C. hoffmanni does not appear to be involved in this mimetic relationship.

Contrasting modes and tempos of venom expression evolution in two snake species.

Selection is predicted to drive diversification within species and lead to local adaptation, but understanding the mechanistic details underlying this process and thus the genetic basis of adaptive evolution requires the mapping of genotype to phenotype. Venom is complex and involves many genes, but the specialization of the venom gland toward toxin production allows specific transcripts to be correlated with specific toxic proteins, establishing a direct link from genotype to phenotype. To determine the extent of expression variation and identify the processes driving patterns of phenotypic diversity, we constructed genotype-phenotype maps and compared range-wide toxin-protein expression variation for two species of snake with nearly identical ranges: the eastern diamondback rattlesnake (Crotalus adamanteus) and the eastern coral snake (Micrurus fulvius). We detected significant expression variation in C. adamanteus, identified the specific loci associated with population differentiation, and found that loci expressed at all levels contributed to this divergence. Contrary to expectations, we found no expression variation in M. fulvius, suggesting that M. fulvius populations are not locally adapted. Our results not only linked expression variation at specific loci to divergence in a polygenic, complex trait but also have extensive conservation and biomedical implications. C. adamanteus is currently a candidate for federal listing under the Endangered Species Act, and the loss of any major population would result in the irrevocable loss of a unique venom phenotype. The lack of variation in M. fulvius has significant biomedical application because our data will assist in the development of effective antivenom for this species.

Phylogeography of Ophryotrocha labronica (Polychaeta, Dorvilleidae) along the Italian coasts

AbstractSpecies of the genus Ophryotrocha are a well‐studied group of organisms but, despite the relatively large body of biological studies, little is known about their intra‐specific patterns of genetic diversity. In the present study, we analysed the patterns of genetic variation in samples of Ophryotrocha labronica (Polychaeta, Dorvilleidae) collected along the Italian coasts within three regions with different thermal regimes: the Northern Adriatic Sea (NAS), the Ligurian Sea (LS), and the South/Southeast Sicilian Sea (SS). A partial sequence of the cytochrome c oxidase subunit I (COI) gene was used as a genetic marker. An analysis of molecular variance (AMOVA) showed significant genetic differentiation between the NAS and the other regions. Conversely, little or no genetic structuring was found between the LS and the SS or amongst locations within a given region. A Bayesian phylogenetic tree and a median‐joining network provided evidence for the occurrence of two highly divergent genetic lineages characterized by a high average sequence divergence (17.2%, Kimura two‐parameter distance). The spatial patterns of genetic variation found in O. labronica may reflect the signature of past expansion events of the two genetic lineages. Although the high sequence divergence suggested that cryptic speciation within O. labronica may have occurred, other traits such as the absence of reproductive isolation, pattern of phenotypic variation and habitat specificity prompted us to regard the two groups as distinct COI lineages of O. labronica.

Non-Metric Dental Traits in Human Skeletal Remains from Transcaucasian Populations: Phylogenetic and Diachronic Evidence

The aim of the study is the assessment of biological distance between populations from Transcaucasia on the basis of the frequency of dental morphological traits. It is well known that these traits are characterised by a high inter-population differentiation, low sexual dimorphism, and their recording is loaded by relatively small intra and inter observer error. The dental morphological traits are successfully used in the description and explanation of the microevolutionary and ethnogenetic processes. This paper presents the results of the odontological differentiation of human populations from Transcaucasia. The comparative analysis was carried out on the basis of 12 groups. From the obtained results, we can draw the following conclusions: The populations of Armenian Highland and Georgia can be differentiated as far as the frequency of dental morphological traits are concerned. They also do not exhibit similar intragroup variability. Biocultural diversity of ancient Transcaucasian populations has not been studied extensively; therefore, delineating some of the patterns of phenotypic variation may be useful for understanding their ongoing evolution.

Pattern of Phenotypic Variation Among Three Populations of Indian Major Carp, Catla catla (Hamilton, 1822) Using Truss Network System in the Ganga Basin, India

Catla catla (Hamilton, 1822) is a commercially important freshwater cyprinid distributed widely in India and adjacent countries. In total 142 specimens of C. catla were collected from three geographically separate watersheds of Ganga basin. A truss network was constructed by interconnecting 12 landmarks to yield 30 distance variables that were extracted from digital images of specimens using tpsDig2 and PAST software. Transformed truss measurements were subjected to univariate analysis of variance, factor analysis and discriminant function analysis (DFA). A total of 28 distance variables exhibited significant differences between the populations. The principal component analysis generated seven components explaining 86.40 % of total intraspecific variance in populations. By applying step-wise DFA, 100 % of the specimens were classified into their original populations (98.5 % under a ‘leave-one-out’ procedure). The occurrence of distinct populations may be due to differences in physical and ecological parameters of the three tributaries of the Ganga basin.

A Generalized Approach to the Modeling and Analysis of 3D Surface Morphology in Organisms

The surface geometry of an organism represents the boundary of its three-dimensional (3D) form and can be used as a proxy for the phenotype. A mathematical approach is presented that describes surface morphology using parametric 3D equations with variables expressed as x, y, z in terms of parameters u, v. Partial differentiation of variables with respect to parameters yields elements of the Jacobian representing tangent lines and planes of every point on the surface. Jacobian elements provide a compact size-free summary of the entire surface, and can be used as variables in principal components analysis to produce a morphospace. Mollusk and echinoid models are generated to demonstrate that whole organisms can be represented in a common morphospace, regardless of differences in size, geometry, and taxonomic affinity. Models can be used to simulate theoretical forms, novel morphologies, and patterns of phenotypic variation, and can also be empirically-based by designing them with reference to actual forms using reverse engineering principles. Although this study uses the Jacobian to summarize models, they can also be analyzed with 3D methods such as eigensurface, spherical harmonics, wavelet analysis, and geometric morphometrics. This general approach should prove useful for exploring broad questions regarding morphological evolution and variation.

Genomic imprinting and parent-of-origin effects on complex traits

Parent-of-origin effects occur when the phenotypic effect of an allele depends on whether it is inherited from the mother or the father. Several phenomena can cause parent-of-origin effects, but the best characterized is parent-of-origin-dependent gene expression associated with genomic imprinting. The development of new mapping approaches applied to the growing abundance of genomic data has demonstrated that imprinted genes can be important contributors to complex trait variation. Therefore, to understand the genetic architecture and evolution of complex traits, including complex diseases and traits of agricultural importance, it is crucial to account for these parent-of-origin effects. Here, we discuss patterns of phenotypic variation associated with imprinting, evidence supporting its role in complex trait variation and approaches for identifying its molecular signatures.

Meta-Analysis of Factors Affecting Ontogenetic Development Rate in theCulex pipiens(Diptera: Culicidae) Complex

Meta-analysis of 33 studies of developmental timing of Culex pipiens s.l. Linnaeus demonstrates that development rate, or the rate of progression through immature life stadia, is primarily driven by temperature, whereas immature survival is driven by temperature, density, and variability in the environmental conditions. As expected, the linear relationship of temperature and development rate is positive for the larval period as well as development to adult emergence. However, the strength of this association varies significantly. Variation in development rate can be explained using additional environmental factors of intraspecific rearing density, sex, and study methodology. Heterogeneity in development rates even once temperature has been considered emphasizes the need for further research of multiple environmental factors and in changing environments. Immature survival is also significantly impacted by variability in environmental conditions. Development rates vary between subspecies of Cx. pipiens, but these population differences are no longer significant once an environmental factor of temperature is considered. Thus, variability in development rate of these insects appears to be primarily driven by response to certain environmental conditions rather than differences between populations. Broad patterns of phenotypic variation across latitude and 96 yr of empirical estimates were not significant once environmental rearing conditions had been considered.

Genetic variation in social influence on mate preferences

Patterns of phenotypic variation arise in part from plasticity owing to social interactions, and these patterns contribute, in turn, to the form of selection that shapes the variation we observe in natural populations. This proximate-ultimate dynamic brings genetic variation in social environments to the forefront of evolutionary theory. However, the extent of this variation remains largely unknown. Here, we use a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae) to assess how mate preferences are influenced by genetic variation in the social environment. We used full-sibling split-families as 'treatment' social environments, and reared focal females alongside each treatment family, describing the mate preferences of the focal females. With this method, we detected substantial genetic variation in social influence on mate preferences. The mate preferences of focal females varied according to the treatment families along with which they grew up. We discuss the evolutionary implications of the presence of such genetic variation in social influence on mate preferences, including potential contributions to the maintenance of genetic variation, the promotion of divergence, and the adaptive evolution of social effects on fitness-related traits.

Spatial and Temporal Drivers of Phenotypic Diversity in Polymorphic Snakes

Color polymorphism in natural populations presents an ideal opportunity to study the evolutionary drivers of phenotypic diversity. Systems with striking spatial, temporal, and qualitative variation in color can be leveraged to study the mechanisms promoting the distribution of different types of variation in nature. We used the highly polymorphic ground snake (Sonora semiannulata), a putative coral snake mimic with both cryptic and conspicuous morphs, to compare patterns of neutral genetic variation and variation over space and time in color polymorphism to investigate the mechanistic drivers of phenotypic variation across scales. We found that strong selection promotes color polymorphism across spatial and temporal scales, with morph frequencies differing markedly between juvenile and adult age classes within a single population, oscillating over time within multiple populations, and varying drastically over the landscape despite minimal population genetic structure. However, we found no evidence that conspicuousness of morphs was related to which color pattern was favored by selection or to any geographic factors, including sympatry with coral snakes. We suggest that complex patterns of phenotypic variation in polymorphic systems may be a fundamental outcome of the conspicuousness of morphs and that explicit tests of temporal and geographic variation are critical to the interpretation of conspicuousness and mimicry.

Speciation in ninespine stickleback: reproductive isolation and phenotypic divergence among cryptic species of Japanese ninespine stickleback

Although similar patterns of phenotypic diversification are often observed in phylogenetically independent lineages, differences in the magnitude and direction of phenotypic divergence have been also observed among independent lineages, even when exposed to the same ecological gradients. The stickleback family is a good model with which to explore the ecological and genetic basis of parallel and nonparallel patterns of phenotypic evolution, because there are a variety of populations and species that are locally adapted to divergent environments. Although the patterns of phenotypic divergence as well as the genetic and ecological mechanisms have been well characterized in threespine sticklebacks, Gasterosteus aculeatus, we know little about the patterns of phenotypic diversification in other stickleback lineages. In eastern Hokkaido, Japan, there are three species of ninespine sticklebacks, Pungitius tymensis and the freshwater type and the brackish-water type of the P. pungitius-P. sinensis species complex. They utilize divergent habitats along coast-stream gradients of rivers. Here, we investigated genetic, ecological and phenotypic divergence among three species of Japanese ninespine sticklebacks. Divergence in trophic morphology and salinity tolerance occurred in the direction predicted by the patterns observed in threespine sticklebacks. However, the patterns of divergence in armour plate were different from those previously found in threespine sticklebacks. Furthermore, the genetic basis of plate variation may differ from that in threespine sticklebacks. Because threespine sticklebacks are well-established model for evolutionary research, the sympatric trio of ninespine sticklebacks will be an invaluable resource for ecological and genetic studies on both common and lineage-specific patterns of phenotypic diversification.

Landscape genetics and spatial pattern of phenotypic variation ofEristalis tenaxacross Europe

A study of population connectivity of the migratory insect species, such as dronefly Eristalis tenax (Diptera, Syrphidae), has an essential importance in understanding the relative influence of the evolutionary forces and environmental features that interact in the spatial distribution of molecular and morphological diversity. However, specific study aiming to understand spatial genetic structure of dronefly populations and its migratory potential is lacking. Hence, we studied a spatial pattern of genetic and phenotypic variation of seven European populations of E. tenax incorporating landscape genetic methods using allozyme data, wing size and shape and abdominal colour pattern. Based on the observed lack of genotypic structuring, we suggested that there has been sufficient long-distance gene flow to effectively homogenize population structuring at a broader geographical scale. Wing shape similarity among populations and an overlap of abdominal colour variation showed no clear clustering related to geography, which is in congruence with genetic data. However, genetic (FST values) and phenotypic (wing size) data and landscape genetics indicated subdivision between the Balkan populations (four Serbian samples) and populations from Central (Germany and Switzerland) and Northern (Finland) Europe. These findings indicated a potential connection between the Central and Northern Europe supporting the Central European origin of the flies caught in Finland. Thus, by performing spatial analysis and combining genetic–morphological approach, we shed light on the movement pattern in complex landscapes and thus provided the necessary guidelines to a broad-scale analysis of this widespread generalist pollinator.

Latitudinal clines in the grasshopperDichroplus elongatus: Coevolution of the A genome and B chromosomes?

Argentine populations of Dichroplus elongatus (Orthoptera: Acrididae) are polymorphic for B chromosomes. Previous studies showed that B chromosomes affect body size and some fitness components in Northwestern populations. We studied phenotype and B's variation patterns along a latitudinal cline as well as the relationship between karyotype and body size related traits in 17 populations from East. Body size related traits showed a 'saw tooth' pattern of variation being small at low and high latitudes and large at intermediate latitudes in most of the analysed populations. Analyses of variance and principal components demonstrated that in most analysed populations B carrier males are associated with a decrease in body size related traits with respect to individuals with standard karyotype. Accordingly with the relationship between karyotype and body size, an opposite pattern of latitudinal variation in the frequencies of B's with respect to body size variation was observed in this area. i.e. smaller individuals tend to have a higher frequency of B chromosomes. The comparison of the differentiation of both karyotype and body size traits with molecular neutral markers demonstrated the relative importance of selection moulding chromosome and phenotype variation. The observed pattern of phenotypic variation is likely to be the result of local adaptation to season length along the latitudinal gradient. The observed contrary pattern of B's clinal variation may reflect the population ability to maintain this chromosome in relation to the local adaptation. The available evidence indicates that the distribution of B chromosome frequency was shaped by selective factors.