Independent evolution of complex life history adaptations in two families of fishes, live-bearing halfbeaks (zenarchopteridae, beloniformes) and poeciliidae (cyprinodontiformes)

We have previously documented multiple, independent origins of placentas in the fish family Poeciliidae. Here we summarize similar analyses of fishes in the family Zenarchopteridae. This family includes three live-bearing genera. Earlier studies documented the presence of superfetation, or the ability to carry multiple litters of young in different stages of development in the same ovary, in some species in all three genera. There is also one earlier report of matrotrophy, or extensive postfertilization maternal provisioning, in two of these genera. We present detailed life-history data for approximately half of the species in all three genera and combine them with the best available phylogeny to make inferences about the pattern of life-history evolution within this family. Three species of Hemirhamphodon have superfetation but lack matrotrophy. Most species in Nomorhamphus and Dermogenys either lack superfetation and matrotrophy or have both superfetation and matrotrophy. Our phylogenetic analysis shows that matrotrophy may have evolved independently in each genus. In Dermogenys, matrotrophic species produce fewer, larger offspring than nonmatrotrophic species. In Nomorhamphus; matrotrophic species instead produce more and smaller offspring than lecithotrophic species. However, the matrotrophic species in both genera have significantly smaller masses of reproductive tissue relative to their body sizes. All aspects of these results are duplicated in the fish family Poeciliidae. We discuss the possible adaptive significance of matrotrophy in the light of these new results. The two families together present a remarkable opportunity to study the evolution of a complex trait because they contain multiple, independent origins of the trait that often include close relatives that vary in either the presence or absence of the matrotrophy or in the degree to which matrotrophy is developed. These are the raw materials that are required for either an analysis of the adaptive significance of the trait or for studies of the genetic mechanisms that underlie the evolution of the trait.     

Detection and stability of quantitative trait loci (QTL) in Eucalyptus globulus

Eucalyptus globulus Labill. ssp. globulus is an important tree species for the pulp and paper industry, and several breeding programmes throughout the world are striving to improve key traits such as growth and wood density. This study aimed to detect quantitative trait loci (QTL) for growth, wood density, relative bark thickness and early flowering in a single full-sib E. globulus family grown across seven sites. Growth was measured a number of times over a 6-year period, enabling temporal stability of growth QTL to be studied. Ten putative QTL (LOD > 2.0) were detected in the single family, which was of moderate size. Based on permutations of the trait data, six of these QTL were significant at the experimentwise significance level of 0.1 for at least one of the four models implemented in analysis to remove site effects. For wood density, two putative QTL explained 20% of the variance for the trait, indicating that a small number of QTL might explain a reasonable proportion of the trait variance. One of these QTL was found to be independent of QTL for growth whereas the second QTL co-segregated with a QTL for relative incremental growth. The marker nearest to this QTL was associated with fast growth but low wood density. A putative growth QTL at year 6 was found to be relatively stable across ages. In addition, it was found that residuals from models based on measurements from across all families across all sites in the trial detected QTL with greater experimentwise significance.     

Asexual propagules as an adaptive trait for epiphylly in tropical leafy liverworts (Lejeuneaceae)

? Premise of the study: Many links between form and function are described in the context of adaptation. Several morphological and life-history traits in the leafy liverwort family Lejeuneaceae (Marchantiophyta) have been hypothesized to be adaptations for living on the surface of leaves of vascular plants (epiphylly). There have been, however, no rigorous tests of these hypotheses. ? Methods: Using a recently published phylogeny of Lejeuneaceae and trait data from published monographs, I tested the correlations of putative adaptive traits with the incidence of epiphylly. Both cross-species and phylogenetic-based analyses of trait data were performed to distinguish the patterns of shared evolutionary history from independent origins of putatively adaptive traits. The rates of transitions between different combinations of character states were also calculated to determine whether traits were more likely to evolve in the presence of epiphylly. ? Key results: Only one trait, production of asexual propagules, was correlated with epiphylly in the phylogenetic-based analysis. The rate of transition to asexual propagules was also significantly higher in the presence of epiphylly. Other traits correlated with epiphylly appeared to be the results of shared evolutionary history among sister taxa and therefore not due to adaptive evolution. ? Conclusion: The present study distinguished production of asexual propagules from other traits as a key adaptive response to living on the leaf surface. No other putative "adaptive" traits to epiphylly showed evidence of being specific adaptation to epiphylly. The results highlight the importance of phylogenetically controlled methods in determining an adaptive function of traits.     

Synthesising the trait information of European Chironomidae (Insecta: Diptera): Towards a new database

Chironomidae are among the most conspicuous and ecological diverse group of freshwater invertebrates. They may dominate unimpacted communities in abundance and biomass, accounting for more than 50% of macroinvertebrate species in standing and flowing waters. In deep zones of eutrophic lakes and highly human-impacted streams, they are often the only family of aquatic insects remaining. In bioassessment programmes, Chironomids are often identified at the family and subfamily levels, due to difficulties in the taxonomic identification of larvae resulting from a high intrinsic morphological similarity. This may potentially result in bias as, similarly to Ephemeroptera, Trichoptera or Plecoptera, Chironomidae species, which are replaced along natural and human-impacted gradients due to differences in their ecological requirements. Recently, multiple trait-based approaches have been proposed to complement taxonomic-based assessment of streams and rivers using macroinvertebrates. However, the lack of specific trait information for Chironomidae prevents their use in the functional assessment of communities. Therefore, here, we aimed to: (1) develop a trait database for European Chironomidae genera that can be used in future bioassessment and ecological studies; (2) evaluate, by multivariate analyses, whether our new database provides additional information on Chironomidae compared to the trait information provided in the commonly used European trait database (Tachet et al., 2010); and (3) determine whether the new information on Eltonian traits (proxy to biological traits) translates the most accepted phylogenetic relationships among Chironomidae subfamilies. We gathered information on 744 species and 178 genera, for 37 traits covering 186 trait categories, and found substantial differences between our database and the commonly used European trait database. In addition, available information on traits was not always in agreement with phylogenetic relationships among subfamilies. Orthocladiinae and Chironominae which are considered sister groups in evolutionary terms actually showed confident trait relatedness based on Eltonian traits tree while the remaining relationships between subfamilies are questionable. In addition, different traits can occur in closely related taxa depending on the environmental drivers operating on their habitats. Our study reveals that the usually accepted redundancy within the Chironomidae family and subfamilies must be a product of averaging the information from finer taxonomic resolution added to the substantial lack of information for this insect group.     

Testing for familial correlation in age-at-onset

The analysis of family-study data sometimes focuses on whether a dichotomous trait tends to cluster in families. For traits with variable age-at-onset, it may be of interest to investigate whether age-at-onset itself also exhibits familial clustering. A complication in such investigations is that censoring by age-at-ascertainment can induce artifactual familial correlation in the age-at-onset of affected members. A further complication can be that sample inclusion criteria involve the affection status of family members. The purpose here is to present an approach to testing for correlation that is not confounded by censoring by age-at-ascertainment and may be applied with a broad range of inclusion criteria. The approach involves regression statistics in which subjects's covariate terms are chosen to reflect age-at-onset information from the subjects's affected family members. The results of analyses of data from a family-study of panic disorder illustrate the approach.     

Phylogenetic analysis of sexual dimorphism and eye-span allometry in stalk-eyed flies (Diopsidae)

Eye stalks and their scaling relationship with body size are important features in the mating system of many diopsid species, and sexual selection is a critical force influencing the evolution of this exaggerated morphology. Interspecific variation in eye span suggests there has been significant evolutionary change in this trait, but a robust phylogenetic hypothesis is required to determine its rate and direction of change. In this study, the pattern of morphological evolution of eye span is assessed in a phylogenetic framework with respect to its function in the sexual system of these flies. Specifically, we examine within the family Diopsidae the pattern of increase and decrease in sexual dimorphism, the morphological coevolution of eye span between males and females, and the evolutionary flexibility of eye-span allometry. Based on several different methods for reconstructing morphological change, results suggest a general pattern of evolutionary flexibility, particularly for eye-span allometry. Sexual dimorphism in eye span has evolved independently at least four times in the family and this trait also has undergone several reductions within the genus Diasemopsis. Despite most species being dimorphic, there is a strong phylogenetic correlation between males and females for mean eye span. The coevolution between the sexes for eye-span allometry, however, is significantly weaker. Overall, eye-span allometry exhibits significantly more change on the phylogeny than the other morphological traits. The evolutionary pattern in eye-span allometry is caused primarily by changes in eye-span variance. Therefore, this pattern is consistent with recent models that predict a strong relationship between sexual selection and the variance of ornamental traits and highlights the significance of eye-span allometry in intersexual and intrasexual signaling.     

ASEXUAL REPRODUCTION IN CESTODES (CYCLOPHYLLIDEA: TAENIIDAE): ECOLOGICAL AND PHYLOGENETIC INFLUENCES

Asexual reproduction, a rare trait among cestodes in general, occurs in the “larval” (metacestode) stage of species of the family Taeniidae. The distribution of this trait among taeniid species is not consistent with an ecological hypothesis of current environmental predictability. We therefore chose a subset of the family and studied their phylogenetic relationships by Wagner parsimony analysis as a test of historical influences on asexual reproduction. We produced a consensus tree based on four 50-step trees with consistency indices of 0.38. Given these hypothetical relationships, we found that asexual reproduction either arose or was lost multiple times. Moreover, this consensus tree is incongruent with both definitive and intermediate host phylogenies, and asexual reproduction does not correlate with host transfers inferred from these phylogenies. Developmental and phylogenetic constraints on asexual reproduction therefore appear to have been minimal. Given current information, neither historical constraint nor explanations invoking adaptation based on environmental predictability can account for life-history variation in these cestodes.     

Permutation methods for the structured exploratory data analysis (SEDA) of familial trait values.

A collection of functions that contrast familial trait values between and across generations is proposed for studying transmission effects and other collateral influences in nuclear families. Two classes of structured exploratory data analysis (SEDA) statistics are derived from ratios of these functions. SEDA-functionals are the empirical cumulative distributions of the ratio of the two contrasts computed within each family. SEDA-indices are formed by first averaging the numerator and denominator contrasts separately over the population and then forming their ratio. The significance of SEDA results are determined by a spectrum of permutation techniques that selectively shuffle the trait values across families. The process systematically alters certain family structure relationships while keeping other familial relationships intact. The methodology is applied to five data examples of plasma total cholesterol concentrations, reported height values, dermatoglyphic pattern intensity index scores, measurements of dopamine-beta-hydroxylase activity, and psychometric cognitive test results.     

Identification and verification of QTL associated with growth traits in two genetic backgrounds of Barramundi (Lates calcarifer)

Quantitative trait loci (QTL) affecting growth traits have previously been mapped in linkage groups (LG) 2, 3 and 23 of Barramundi ( Lates carcalifer ), but these QTL have not been verified in different genetic backgrounds and environments. Here, we report the identification and verification of QTL for growth traits on LG2, 3, 10 and 23 in F₁ families constructed using brooders from the Singapore Marine Aquaculture Center (MAC) and from wild stocks collected in Thailand (THAI). The previously detected QTL for body weight and length linked to marker Lca371 on LG2 were confirmed in both the MAC and THAI families, whereas other QTL previously mapped to LG3 and 23 were only detected in one of the two families. QTL for body weight and length were identified in the MAC family, but not in the THAI family, in a region where the insulin-like growth factor 2 ( IGF2 ) and tyrosine hydroxylase 1 ( TH1 ) genes are located on LG10. Significant epistatic interactions were identified between markers Lca287 on LG2 and IGF2 on LG10 for growth trait QTL in the MAC family, but not in the THAI family. Effects of the IGF2 , TH1 and parvalbumin 1 candidate genes were family-specific. Our results indicate that some but not all QTL are family-specific in Barramundi.     

A 1927 study supports a current genetic model for inheritance of human scalp hair-whorl orientation and hand-use preference traits

The basis of right- vs. left-hand-use preference in humans has been debated for a long time. Culturally learned, birth stress, and biologically specified causes are the prominent etiologies under consideration. A 2003 (Klar 2003) study reported a correlation between a person's preferred hand and the scalp hair-whorl orientation developed on the head. By reinterpreting results of a 1927 (Schwarzburg 1927) study on the genetics of the hair-whorl trait, support for a recent single gene, two-allele "random-recessive model" for both hair-whorl orientation and handedness trait inheritance is demonstrated.     

Association of the heart fatty acid-binding protein (FABP3) gene with milk traits in Manchega breed sheep

The ovine fatty acid-binding protein type 3 gene has been chosen as a functional candidate gene for milk traits. Two different single nucleotide polymorphisms (SNPs) of ovine FABP3 gene have been tested in a daughter design comprising 13 families. No association was found between estimated breeding values for milk yield, protein and fat contents (FC) and genotypes across families using anova and transmission disequilibrium test (TDT). In within-family analysis, one family showed a significant effect for FC. These results could indicate linkage disequilibrium between the FABP3 gene and a quantitative trait loci (QTL) for FC, with the heterozygous genotype associated with a positive effect in this trait.     

Quantitative Trait Loci (QTL) and Mendelian Trait Loci (MTL) Analysis in Prunus: a Breeding Perspective and Beyond

Trait loci analysis, a classic procedure in quantitative (quantitative trait loci, QTL) and qualitative (Mendelian trait loci, MTL) genetics, continues to be the most important approach in studies of gene labeling in Prunus species from the Rosaceae family. Since 2011, the number of published Prunus QTLs and MTLs has doubled. With increased genomic resources, such as whole genome sequences and high-density genotyping platforms, trait loci analysis can be more readily converted to markers that can be directly utilized in marker-assisted breeding. To provide this important resource to the community and to integrate it with other genomic, genetic, and breeding data, a global review of the QTLs and MTLs linked to agronomic traits in Prunus has been performed and the data made available in the Genome Database for Rosaceae. We describe detailed information on 760 main QTLs and MTLs linked to a total of 110 agronomic traits related to tree development, pest and disease resistance, flowering, ripening, and fruit and seed quality. Access to these trait loci enables the application of this information in the post-genomic era, characterized by the availability of a high-quality peach reference genome and new high-throughput DNA and RNA analysis technologies.     

Segregation of genetic hemochromatosis indexed by latent capacity of transferrin.

A genetic analysis of the segregation of hereditary hemochromatosis, indexed by the measurement of latent capacity of transferrin (LCAP), was undertaken in an ascertained sample of 147 pedigrees from Brittany, France. There were no mean differences by sex in the distribution of LCAP in the control sample, although in the family data there was a higher representation of males with low values than of females with low values, consistent with the higher proportion of affected males. The results of bivariate segregation analysis revealed no systematic evidence for heterozygous expression either in the biochemical domain of LCAP abnormalities or in increased liability to overt symptomatic disease. Joint consideration of the quantitative variable with hemochromatosis affection status allowed clear resolution of a recessive single-gene inheritance pattern in these families.     

Power of two and three-generation QTL mapping experiments in an outbred population containing full-sib or half-sib families

QTL mapping experiments involve many animals to be genotyped and performance tested. Consequently, experimental designs need to be optimized to minimize the costs of data collection and genotyping. The present study has analyzed the power and efficiency of experiments with two or three-generation family structures containing full-sib families, half-sib families, or both. The focus was on data from one outbred population because the main interest is to locate genes that can be used for within-line selection. For a two generation experiment more animals had to be typed for marker loci to obtain a certain power than for a three generation experiment. Fewer trait values, however, had to be obtained for a two-generation experiment than for a three-generation experiment. A two or three-generation family structure with full-sib offspring was more efficient than a two or three-generation family structure with half-sib offspring. A family structure with full-sib grand-offspring, however, was less efficient than a family structure with half-sib grand-offspring. For the most efficient family structure each pair of parents had full-sib offspring that were genotyped for the marker. For the most-efficient family structure each full-sib offspring had half-sib grand-offspring for which trait values were obtained. For equal power with a heritability of 0.1 and 100 grand-offspring per full-sib offspring, 30-times less marker typings were required for this most efficient family structure than for a two-generation half-sib structure in which marker genotypes and trait values were obtained for half-sib offspring. The effect of heritability and the type of analysis (single marker or interval analysis) on the efficiency of a family structure is described. The results of this study should help to design QTL mapping experiments in an outbred population.     

Linkage analysis of the GAW14 simulated dataset with microsatellite and single-nucleotide polymorphism markers in large pedigrees

Recent studies have suggested that a high-density single nucleotide polymorphism (SNP) marker set could provide equivalent or even superior information compared with currently used microsatellite (STR) marker sets for gene mapping by linkage. The focus of this study was to compare results obtained from linkage analyses involving extended pedigrees with STR and single-nucleotide polymorphism (SNP) marker sets. We also wanted to compare the performance of current linkage programs in the presence of high marker density and extended pedigree structures. One replicate of the Genetic Analysis Workshop 14 (GAW14) simulated extended pedigrees (n = 50) from New York City was analyzed to identify the major gene D2. Four marker sets with varying information content and density on chromosome 3 (STR [7.5 cM]; SNP [3 cM, 1 cM, 0.3 cM]) were analyzed to detect two traits, the original affection status, and a redefined trait more closely correlated with D2. Multipoint parametric and nonparametric linkage analyses (NPL) were performed using programs GENEHUNTER, MERLIN, SIMWALK2, and S.A.G.E. SIBPAL. Our results suggested that the densest SNP map (0.3 cM) had the greatest power to detect linkage for the original trait (genetic heterogeneity), with the highest LOD score/NPL score and mapping precision. However, no significant improvement in linkage signals was observed with the densest SNP map compared with STR or SNP-1 cM maps for the redefined affection status (genetic homogeneity), possibly due to the extremely high information contents for all maps. Finally, our results suggested that each linkage program had limitations in handling the large, complex pedigrees as well as a high-density SNP marker set.     

Linkage mapping of a complex trait in the New York population of the GAW14 simulated dataset: a multivariate phenotype approach

Multivariate phenotypes underlie complex traits. Thus, instead of using the end-point trait, it may be statistically more powerful to use a multivariate phenotype correlated to the end-point trait for detecting linkage. In this study, we develop a reverse regression method to analyze linkage of Kofendrerd Personality Disorder affection status in the New York population of the Genetic Analysis Workshop 14 (GAW14) simulated dataset. When we used the multivariate phenotype, we obtained significant evidence of linkage near four of the six putative loci in at least 25% of the replicates. On the other hand, the linkage analysis based on Kofendrerd Personality Disorder status as a phenotype produced significant findings only near two of the loci and in a smaller proportion of replicates.     

Evolution and losses of spines in slug caterpillars (Lepidoptera: Limacodidae)

Larvae of the cosmopolitan family Limacodidae, commonly known as “slug” caterpillars, are well known because of the widespread occurrence of spines with urticating properties, a morpho‐chemical adaptive trait that has been demonstrated to protect the larvae from natural enemies. However, while most species are armed with rows of spines (“nettle” caterpillars), slug caterpillars are morphologically diverse with some species lacking spines and thus are nonstinging. It has been demonstrated that the evolution of spines in slug caterpillars may have a single origin and that this trait is possibly derived from nonstinging slug caterpillars, but these conclusions were based on limited sampling of mainly New World taxa; thus, the evolution of spines and other traits within the family remains unresolved. Here, we analyze morphological variation in slug caterpillars within an evolutionary framework to determine character evolution of spines with samples from Asia, Australia, North America, and South America. The phylogeny of the Limacodidae was reconstructed based on a multigene dataset comprising five molecular markers (5.6 Kbp: COI, 28S, 18S, EF‐1α, and wingless) representing 45 species from 40 genera and eight outgroups. Based on this phylogeny, we infer that limacodids evolved from a common ancestor in which the larval type possessed spines, and then slug caterpillars without spines evolved independently multiple times in different continents. While larvae with spines are well adapted to avoiding generalist predators, our results imply that larvae without spines may be suited to different ecological niches. Systematic relationships of our dataset indicate six major lineages, several of which have not previously been identified.     

Individualized Iterative Phenotyping for Genome-wide Analysis of Loss-of-Function Mutations

Next-generation sequencing provides the opportunity to practice predictive medicine based on identified variants. Putative loss-of-function (pLOF) variants are common in genomes and understanding their contribution to disease is critical for predictive medicine. To this end, we characterized the consequences of pLOF variants in an exome cohort by iterative phenotyping. Exome data were generated on 951 participants from the ClinSeq cohort and filtered for pLOF variants in genes likely to cause a phenotype in heterozygotes. 103 of 951 exomes had such a pLOF variant and 79 participants were evaluated. Of those 79, 34 had findings or family histories that could be attributed to the variant (28 variants in 18 genes), 2 had indeterminate findings (2 variants in 2 genes), and 43 had no findings or a negative family history for the trait (34 variants in 28 genes). The presence of a phenotype was correlated with two mutation attributes: prior report of pathogenicity for the variant (p = 0.0001) and prior report of other mutations in the same exon (p = 0.0001). We conclude that 1/30 unselected individuals harbor a pLOF mutation associated with a phenotype either in themselves or their family. This is more common than has been assumed and has implications for the setting of prior probabilities of affection status for predictive medicine.     

The roles of environment,space, and phylogeny in determining functional dispersion of rodents (Rodentia) in the Hengduan Mountains,China

The recently described trait‐based approach is becoming widely popular for a mechanistic understanding of species coexistence. However, the greatest challenge in functional analyses is decomposing the contributions of different ecological and evolutionary processes (e.g., niche‐based process, neutral process, and evolutionary process) in determining trait structure. Taking rodents (Rodentia) in the Hengduan Mountains as our study model, we aim to (1) quantify the vertical patterns of functional structure for head–body length (HL), tail/body ratio (TR), animal component in diet (ACD), and all traits; (2) disentangle the relative importance of different assembly processes (environment, space, and phylogeny) in structuring trait dispersion; and (3) assess the feasibility of Bergmann's rule and Allen's rule along elevational gradient. Our results have suggested that the vertical functional structure pattern varied across these three traits, indicating distinct functional roles in the community assembly process. These nonrandom vertical patterns of HL, TR, and terminal ACD have demonstrated these traits were dominated by different ecological process along environmental gradient. In variance partitioning, high proportion of the spatial variations in trait dispersion was explained by environmental and spatial models, which have provided supporting strong evidence for niche‐based and neutral processes in leading species coexistence. Although the three traits all exhibited apparent phylogenetic signals, phylogenetic relationship within community failed to predict the spatial variations of functional dispersion, confirming the enormous inference of phylogenetic signals in predicting trait structure. By assessing the vertical patterns of HL and TR at order and family levels, we argued that functional adaptation along an environmental gradient is a surrogate of series of complex processes (e.g., environmental filtering, interspecific interaction, and neutral dispersal) acting on multiple functional axes, which results in inconsistence with the empirical rules along elevational gradient.     

Structured exploratory data analysis (SEDA) of finger ridge-count inheritance: II. Association arrays in parent-offspring and sib-sib pairs

Familial similarity of the dermatoglyphic trait values of finger ridge-count scores and pattern intensity index is examined for 125 nuclear families from the Velanadu Brahmin population of Southern India by the method of association arrays. This methodology assesses parent-offspring and sibship similarity through a collection of measures of dependence that is sensitive to a variety of nonlinear trends and stochastic relationships between trait values. The method is used in conjunction with various weights to determine the relationship between family size and the level and form of dependence. These analyses reveal that siblings are most strongly associated for ridge-counts of the middle digit and less associated for the thumb and fifth digit ridge-counts. Further, sibship similarity for ridge-counts increases with family size for the thumb and fifth digit but remains relatively constant over all family sizes for the middle finger. Family size effects are also observed for total ridge-counts of the left hand, right hand, and both hands combined, and for the pattern intensity index. These effects of family size may be due to the most pronounced changes occurring in the amniotic environment between the first and second pregnancy, which are most strongly manifested in the sibship associations of smaller families.