Exploring the correlations between sequence evolution rate and phenotypic divergence across the Mammalian tree provides insights into adaptive evolution

Sequence evolution behaves in a relatively consistent manner, leading to one of the fundamental paradigms in biology, the existence of a ??molecular clock??. The molecular clock can be distilled to the concept of accumulation of substitutions, through time yielding a stable rate from which we can estimate lineage divergence. Over the last 50?years, evolutionary biologists have obtained an in-depth understanding of this clock??s nuances. It has been fine-tuned by taking into account the vast heterogeneity in rates across lineages and genes, leading to ??relaxed?? molecular clock methods for timetree reconstruction. Sequence rate varies with life history traits including body size, generation time and metabolic rate, and we review recent studies on this topic. However, few studies have explicitly examined correlates between molecular evolution and morphological evolution. The patterns observed across diverse lineages suggest that rates of molecular and morphological evolution are largely decoupled. We discuss how identifying the molecular mechanisms behind rapid functional radiations are central to understanding evolution. The vast functional divergence within mammalian lineages that have relatively ??slow?? sequence evolution refutes the hypotheses that pulses in diversification yielding major phenotypic change are the result of steady accumulation of substitutions. Patterns rather suggest phenotypic divergence is likely caused by regulatory alterations mediated through mechanisms such as insertions/deletions in functional regions. These can rapidly arise and sweep to fixation faster than predicted from a lineage??s sequence neutral substitution rate, enabling species to leapfrog between phenotypic ??islands??. We suggest research directions that could illuminate mechanisms behind the functional diversity we see today.     

Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines (Open Access publication)

We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL) regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed F_st values greater than 0.15. However, the non-significant difference (P > 0.05) between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone.     

Fine-scale genetic breaks driven by historical range dynamics and ongoing density-barrier effects in the estuarine seaweed Fucus ceranoides L.

Background

In the laboratory, the Drosophila melanogaster heat shock protein Hsp90 can buffer the phenotypic effects of genetic variation. Laboratory experiments either manipulate Hsp90 activity pharmacologically, or they induce mutations with strong effects in the gene Hsp83, the single-copy fly gene encoding Hsp90. It is unknown whether observations from such laboratory experiments are relevant in the wild.

Results

We here study naturally occurring mutations in Hsp83, and their effects on fitness and phenotypic buffering in flies derived from wild populations. We examined more than 4500 flies from 42 Drosophila populations distributed world-wide for insertions or deletions of mobile DNA in or near the Hsp83 gene. The insertions we observed occur at low population frequencies, and reduce Hsp83 gene expression. In competition experiments, mutant flies performed much more poorly than wild-type flies. Mutant flies were also significantly less fecund and shorter-lived than wild-type flies, as well as less well buffered against cryptic deleterious variation, as we show through inbreeding experiments. Specifically, in Hsp83 mutant flies female fecundity dropped to much lower levels after inbreeding than in wild-type flies. At even slightly elevated temperatures, inbred mutant Hsp83 populations went extinct, whereas inbred wild-type populations persisted.

Conclusions

Our work shows that Hsp90, a regulator of the stress response and of signaling, helps buffer deleterious variation in fruit flies derived from wild population, and that its buffering role becomes even more important under heat stress.     

Fly wing evolution explained by a neutral model with mutational pleiotropy

To what extent the speed of mutational production of phenotypic variation determines the rate of long-term phenotypic evolution is a central question. Houle et al. recently addressed this question by studying the mutational variances, additive genetic variances, and macroevolution of locations of vein intersections on fly wings, reporting very slow phenotypic evolution relative to the rates of mutational input, high phylogenetic signals, and a strong, linear relationship between the mutational variance of a trait and its rate of evolution. Houle et al. found no existing model of phenotypic evolution to be consistent with all these observations, and proposed the improbable scenario of equal influence of mutational pleiotropy on all traits. Here, we demonstrate that the purported linear relationship between mutational variance and evolutionary divergence is artifactual. We further show that the data are explainable by a simple model in which the wing traits are effectively neutral at least within a range of phenotypic values but their evolutionary rates are differentially reduced because mutations affecting these traits are purged owing to their different pleiotropic effects on other traits that are under stabilizing selection. Thus, the evolutionary patterns of fly wing morphologies are explainable under the existing theoretical framework of phenotypic evolution.     

Male eyespan size is associated with meiotic drive in wild stalk-eyed flies (Teleopsis dalmanni)

This study provides the first direct evidence from wild populations of stalk-eyed flies to support the hypothesis that male eyespan is a signal of meiotic drive. Several stalk-eyed fly species are known to exhibit X-linked meiotic drive. A recent quantitative trait locus analysis in Teleopsis dalmanni found a potential link between variation in male eyespan, a sexually selected ornamental trait, and the presence of meiotic drive. This was based on laboratory populations subject to artificial selection for male eyespan. In this study, we examined the association between microsatellite markers and levels of sex ratio bias (meiotic drive) in 12 wild T. dalmanni populations. We collected two data sets: (a) brood sex ratios of wild-caught males mated to standard laboratory females and (b) variation in a range of phenotypic traits associated with reproductive success of wild-caught males and females. In each case, we typed individuals for eight X-linked microsatellite markers, including several that previously were shown to be associated with male eyespan and meiotic drive. We found that one microsatellite marker was very strongly associated with meiotic drive, whereas a second showed a weaker association. We also found that, using both independent data sets, meiotic drive was strongly associated with male eyespan, with smaller eyespan males being associated with more female-biased broods. These results suggest that mate preference for exaggerated male eyespan allows females to avoid mating with males carrying the meiotic drive gene and is thus a potential mechanism for the maintenance and evolution of female mate preference.     

Selectionism and neutralism in molecular evolution

Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism. Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions. This suggestion generated an intense controversy over selectionism and neutralism. This controversy is partially caused by Kimura's definition of neutrality, which was too strict (|2Ns|< or =1). If we define neutral mutations as the mutations that do not change the function of gene products appreciably, many controversies disappear because slightly deleterious and slightly advantageous mutations are engulfed by neutral mutations. The ratio of the rate of nonsynonymous nucleotide substitution to that of synonymous substitution is a useful quantity to study positive Darwinian selection operating at highly variable genetic loci, but it does not necessarily detect adaptively important codons. Previously, multigene families were thought to evolve following the model of concerted evolution, but new evidence indicates that most of them evolve by a birth-and-death process of duplicate genes. It is now clear that most phenotypic characters or genetic systems such as the adaptive immune system in vertebrates are controlled by the interaction of a number of multigene families, which are often evolutionarily related and are subject to birth-and-death evolution. Therefore, it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is some similarity between phenotypic and molecular evolution with respect to functional or environmental constraints and evolutionary rate. It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels.     

Genes Belonging to the Insulin and Ecdysone Signaling Pathways Can Contribute to Developmental Time,Lifespan and Abdominal Size Variation in Drosophila americana

Even within a single genus, such as Drosophila, cases of lineage-specific adaptive evolution have been found. Therefore, the molecular basis of phenotypic variation must be addressed in more than one species group, in order to infer general patterns. In this work, we used D. americana, a species distantly-related to D. melanogaster, to perform an F2 association study for developmental time (DT), chill-coma recovery time (CRT), abdominal size (AS) and lifespan (LS) involving the two strains (H5 and W11) whose genomes have been previously sequenced. Significant associations were found between the 43 large indel markers developed here and DT, AS and LS but not with CRT. Significant correlations are also found between DT and LS, and between AS and LS, that might be explained by variation at genes belonging to the insulin and ecdysone signaling pathways. Since, in this F2 association study a single marker, located close to the Ecdysone receptor (EcR) gene, explained as much as 32.6% of the total variation in DT, we performed a second F2 association study, to determine whether large differences in DT are always due to variation in this genome region. No overlapping signal was observed between the two F2 association studies. Overall, these results illustrate that, in D. americana, pleiotropic genes involved in the highly-conserved insulin and ecdysone signaling pathways are likely responsible for variation observed in ecologically relevant phenotypic traits, although other genes are also involved.     

Incipient sexual isolation among cosmopolitan Drosophila melanogaster populations

Understanding the biological conditions and the genetic basis of early stages of sexual isolation and speciation is an outstanding question in evolutionary biology. It is unclear how much genetic and phenotypic variation for mating preferences and their phenotypic cues is segregating within widespread and human-commensal species in nature. A recent case of incipient sexual isolation between Zimbabwe and cosmopolitan populations of the human-commensal fruit fly Drosophila melanogaster indicates that such species may initiate the process of sexual isolation. However, it is still unknown whether other geographical populations have undergone evolution of mating preferences. In this study we present new data on multiple-choice mating tests revealing partial sexual isolation between the United States and Caribbean populations. We relate our findings to African populations, showing that Caribbean flies are partially sexually isolated from Zimbabwe flies, but mate randomly with West African flies, which also show partial sexual isolation from the United States and Zimbabwe flies. Thus, Caribbean and West African populations seem to exhibit distinct mating preferences relative to populations in the United States and in Zimbabwe. These results suggest that widespread and human-commensal species may harbor different types of mating preferences across their geographical ranges.     

Eye pigments of the blood-sucking insect, Triatoma infestans Klug (Hemiptera, Reduviidae).

The pigmentation of black (wild) and red (mutant) eyes of Triatoma infestans was studied spectrophotometrically and compared with red-eyed (wild) and white-eyed (mutant) forms of Drosophila melanogaster. The spectral absorption profiles of the black and red eye pigments of T. infestans were similar to each other and to that of the wild-type eyes of D. melanogaster. The similarity to the wild form of D. melanogaster indicated that both eye forms of T. infestans contained ommochromes of the xanthommatin type, a finding confirmed by ascending paper chromatography. Pteridines, melanins, and ommins were not detected as eye pigments in T. infestans. The eye color difference in T. infestans was assumed to be a function of the xanthommatin concentration, with a smaller content of ommochrome in red eyes, although this probably did not affect the insect's visual acuity. These data support other findings regarding the similarities between black- and red-eyed specimens of T. infestans for other characteristics.     

Proximal fate marker homothorax marks the lateral extension of stalk‐eyed fly Cyrtodopsis whitei

The placement of eyes on insect head is an important evolutionary trait. The stalk‐eyed fly, Cyrtodopsis whitei, exhibits a hypercephaly phenotype where compound eyes are located on lateral extension from the head while the antennal segments are placed inwardly on this stalk. This stalk‐eyed phenotype is characteristic of the family Diopsidae in the Diptera order and dramatically deviates from other dipterans, such as Drosophila. Like other insects, the adult eye and antenna of stalk‐eyed fly develop from a complex eye‐antennal imaginal disc. We analyzed the markers involved in proximo‐distal (PD) axis of the developing eye imaginal disc of the stalk‐eyed flies. We used homothorax (hth) and distalless (dll), two highly conserved genes as the marker for proximal and distal fate, respectively. We found that lateral extensions between eye and antennal field of the stalk‐eyed fly's eye‐antennal imaginal disc exhibit robust Hth expression. Hth marks the head specific fate in the eye‐ and proximal fate in the antenna‐disc. Thus, the proximal fate marker Hth expression evolves in the stalk‐eyed flies to generate lateral extensions for the placement of the eye on the head. Moreover, during pupal eye metamorphosis, the lateral extension folds back on itself to place the antenna inside and the adult compound eye on the distal tip. Interestingly, the compound eye in other insects does not have a prominent PD axis as observed in the stalk‐eyed fly.     

Evolution and Biogeography: Leading Students in Darwin’s and Wallace’s Footsteps

Exploring life??s diversity and geography??s effect on it was central to Darwin and Wallace??s parallel discoveries of evolution. Those discoveries required the two to overcome their own misconceptions about species and biology. By helping students to see the world through the eyes of explorers and placing life??s diversity into a geographic context, teachers can help students overcome those same barriers to the acceptance of evolution and deepen students?? appreciation of biodiversity.     

Crouching variation revealed

The term ‘phenotypic capacitance’ was introduced nearly 15 years ago to describe the strain‐specific effects of impairing Hsp90, a molecular chaperone, in the fly Drosophila melanogaster (Rutherford & Lindquist 1998 ). In one genetic background, Hsp90 depletion caused deformed eyes, whereas in other genetic backgrounds, the wings or abdomens or other aspects of morphology were affected. Hsp90 was therefore viewed as acting like a capacitor, allowing genetic differences to build up and to be released at a later time. In the years since, it has been debated whether capacitance is a laboratory curiosity or a major force in evolution. In this issue of Molecular Ecology, Takahashi ( 2013 ) presents evidence, from high‐resolution morphometric analysis of fly wings, that a large number of other capacitors exist in D. melanogaster, and that the variation they reveal can be quite subtle. His results advance our understanding of capacitance and contribute to a new view of its role in evolutionary adaptation.     

Glycosidases in the plasma membrane of Ceratitis capitata spermatozoa

Fruit flies in the family Tephritidae are rated among the world’s most destructive agricultural pests. The Mediterranean fruit fly Ceratitis capitata is emerging as a model organism to study the fertilization in Insects. Three integral proteins with glycosidase activity are present in the plasma membrane of spermatozoa. The glycosidases have been purified and characterized. We have demonstrated the presence of three enzymes, a ??-N-acetylhexosaminidase, an ??-mannosidase and an ??-l-fucosidase. The molecular mass of the native enzymes estimated by gel filtration was 160 kDa for ??-N-acetylhexosaminidase, 310 kDa for ??-mannosidase and 140 kDa for ??-l-fucosidase. SDS-PAGE showed that ??-N-acetylhexosaminidase is a dimer of a single protein of 73 kDa, ??-mannosidase consists of six subunits with different molecular weights and ??-l-fucosidase is a dimer made up by two different monomers. Characterization of the purified enzymes included glycosylation pattern, pI, optimal pH, substrate preference, kinetic properties and thermal stability. Soluble forms similar to the sperm associated glycosidases are present. Polyclonal antibodies raised against synthetic peptides designed from the predicted products of the Drosophila melanogaster genes encoding ??-N-acetylhexosaminidase and ??-l-fucosidase were used. Immunofluorescence labelling of spermatozoa showed that the enzymes are present in the sperm plasma membrane overlying the acrosome and the tail. This work represents the first report on the characterization in C. capitata of sperm proteins that are potentially involved in primary gamete recognition.     

Fast phototaxis and electroretinograms in red-eyed and white-eyed retinal degeneration mutants of Drosophila melanogaster

Due to the presence or absence of screening pigments red-eyed and white-eyed Drosophila melanogaster have electroretinograms with different sensitivity spectra (Stark and Wassermann, 1974). The same differences were found in a comparison of ERGs of red-eyed and white-eyed retinal degeneration mutants. No effect of the pigments can, however, be found in the spectral sensitivity of escape phototaxis behaviour. The observations imply that only receptor cells in on-axis ommatidia contribute to this behaviour even in the white-eyed fly.     

Colour in the eyes of insects

Many insect species have darkly coloured eyes, but distinct colours or patterns are frequently featured. A number of exemplary cases of flies and butterflies are discussed to illustrate our present knowledge of the physical basis of eye colours, their functional background, and the implications for insect colour vision. The screening pigments in the pigment cells commonly determine the eye colour. The red screening pigments of fly eyes and the dorsal eye regions of dragonflies allow stray light to photochemically restore photoconverted visual pigments. A similar role is played by yellow pigment granules inside the photoreceptor cells which function as a light-controlling pupil. Most insect eyes contain black screening pigments which prevent stray light to produce background noise in the photoreceptors. The eyes of tabanid flies are marked by strong metallic colours, due to multilayers in the corneal facet lenses. The corneal multilayers in the gold-green eyes of the deer fly Chrysops relictus reduce the lens transmission in the orange-green, thus narrowing the sensitivity spectrum of photoreceptors having a green absorbing rhodopsin. The tapetum in the eyes of butterflies probably enhances the spectral sensitivity of proximal long-wavelength photoreceptors. Pigment granules lining the rhabdom fine-tune the sensitivity spectra.     

Bovine thelaziasis in Iowa

The prevalence of developing Thelazia nematodes in face flies (Musca autumnalis) was studied for 7 yr at a beef farm in central Iowa. Juvenile nematodes were not found among flies in reproductive diapause in autumn, nor among nulliparous, overwintered flies in spring, but only among actively reproducing insects. Thus Thelazia probably do not overwinter in face flies. A mean prevalence of 2.0% infected was recorded among flies in 7 fly breeding seasons. No heterogeneity in Thelazia prevalence was detected within fly breeding seasons. The frequency distribution of Thelazia among face flies by year of occurrence was homogeneous, with a mean of 2.75 larval nematodes per infected fly. Thelazia gulosa and T. skrjabini were recovered in necropsy from the eyes of bovines from central Iowa. Prevalence among fat cattle 18-27 mo old was 15%; among cows 3-15 yr old, prevalence was only 3%. Thelazia skrjabini was found in 29 eyes and T. gulosa in 4 eyes. Infections were randomly distributed among the eyes of subject cattle. The mean worm burden was 2.3 T. skrjabini and 12 T. gulosa per infected eye. Thelaziasis is clearly enzootic in Iowa.     

Red-eyed dilution (rd), a novel coat-color mutant gene in the musk shrew (Suncus murinus, Insectivora).

A novel coat-color mutant was found in the musk shrew (Suncus murinus). Mutant shrews were characterized by light-gray coat, pinkish skin and red eyes. Mating experiment demonstrated that the mutant character was controlled by a single autosomal recessive gene. The gene could be traced back to at least four heterozygous carriers captured in Naha city, Okinawa in 1983. The name, red-eyed dilution, was proposed for this mutant character with the gene symbol rd. Linkage analysis proved no close relationship of the rd locus with the cr (cream coat color) and ch (curly hair) loci. The red-eyed dilution shrews (+/+, rd/rd) could easily be distinguished from the cream coat shrews with dark-red eyes (cr/cr, +/+) and the double homozygotes exhibiting light-cream coat with pink eyes (cr/cr, rd/rd). The rd gene has been maintained in the OKI line about at 75% of its frequency in every generation. We have started to develop a new line triple-homozygous for the cr, ch and rd genes.     

Estimating the speed of Drosophila locomotion using an automated behavior detection and analysis system

A fundamental phenotypic trait in Drosophila melanogaster is the speed of movement. Its quantification in response to environmental and experimental factors is highly useful for behavioral and neurological studies. Quantifying this behavioral characteristic in freely moving flies is difficult, and many current systems are limited to evaluating the speed of movement of one fly at a time or rely on expensive, time-consuming methods. Here, we present a novel signal processing method of quantifying the speed of multiple flies using a system with automatic behavior detection and analysis that we previously developed to quantify general activity. By evaluating the shape of the signal wave from recordings of a live and simulated single fly, a metric for speed of movement was found. The feasibility of using this metric to estimate the speed of movement in a population of flies was then confirmed by evaluating recordings taken from populations of flies maintained at two different temperatures. The results were consistent with those reported in the literature. This method provides an automated way of measuring speed of locomotion in a fly population, which will further quantify fly behavioral responses to the environment.