Nuclear DNA divergence among Lathyrus species

Among diploid Lathyrus species a threefold variation in nuclear DNA amount is attributable to differences in the amount of repetitive DNA. Cross reassociation among repetitive and among non-repetitive DNA fractions from different species shows substantial divergence in DNA composition. The divergence in base composition is correlated with nuclear DNA amount. The degree of divergence is of the same order of magnitude in both the repetitive and nonrepetitive fractions.     

Rapid sequence divergence in a heat shock locus of Drosophila

In situ hybridization of cRNA transcribed from cloned D. melanogaster heat shock sequences to D. hydei chromosomes has shown that the D. hydei locus 2–32 A corresponds to the D. melanogaster locus 87 A/C and the D. hydei locus 2–36 A to the D. melanogaster locus 95 D, while the D. hydei locus 4–81 B corresponds to the D. melanogaster locus 63 BC. No hybridization to D. hydei chromosomes was found with cRNA transcribed from a clone containing the sequences encoded by the D. melanogaster locus 87 C. Neither D. melanogaster heat shock RNA nor D. virilis heat shock RNA hybridized significantly to the D. hydei heat shock locus 2–48 B. Furthermore, D. hydei heat shock RNA did not hybridize to the cytological homologs of locus 2–48 B found in D. repleta or in D. virilis. D, hydei heat shock. RNA did hybridize to the cytological homologs of locus 2–48 B in D. neohydei and D. eohydei, both of which belong to the hydei subgroup.     

Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome

The recent sequencing of several eukaryotic genomes has generated considerable interest in the study of gene duplication events. The classical model of duplicate gene evolution is that recurrent mutation ultimately results in one copy becoming a pseudogene, and only rarely will a beneficial new function evolve. Here, we study divergence between coding sequence duplications in Drosophila melanogaster as a function of the linkage relationship between paralogs. The mean K(a)/K(s) between all duplicates in the D. melanogaster genome is 0.2803, indicating that purifying selection is maintaining the structure of duplicate coding sequences. However, the mean K(a)/K(s) between duplicates that are both on the X chromosome is 0.4701, significantly higher than the genome average. Further, the distribution of K(a)/K(s) for these X-linked duplicates is significantly shifted toward higher values when compared with the distributions for paralogs in other linkage relationships. Two models of molecular evolution provide qualitative explanations of these observations-relaxation of selective pressure on the duplicate copies and, more likely, positive selection on recessive adaptations. We also show that there is an excess of X-linked duplicates with low K(s), suggesting a larger proportion of relatively young duplicates on the D. melanogaster X chromosome relative to autosomes.     

Allozyme divergence among species ofWolffia (Lemnaceae)

The genusWolffia was surveyed electrophoretically at 14 allozyme loci. A total of 133 clones representing 10 of the 11 recognized species was examined. Genetic identities among most pairs of species are zero, with non-zero values ranging from 0.14 to 0.40.Wolffia angusta and the newly describedW. neglecta show the highest similarity, and the former species has an identity of 0.14 withW. australiana. The next highest similarity (0.34) occurs betweenW. globosa of Southeast Asia andW. cylindracea of southern Africa, which until recently, had generally been viewed as members of the same species. Other species showing some common alleles are members of a complex involvingW. arrhiza, W. columbiana, W. cylindracea, andW. globosa. WithinW. arrhiza, plants from South Africa and Europe are easily distinguished electrophoretically because each contains unique alleles at two loci. Strains from other parts of Africa vary at these loci and are not totally distinct from either the plants from South Africa or from Europe. Species ofWolffia are much more divergent at allozyme loci than the majority of congeners of flowering plants. This suggests that the species are quite old and that the difficulties in distinguishing taxa morphologically are the result of reduction rather than lack of divergence due to recent speciation. Because of the lack of shared alleles between the majority of species pairs inWolffia, enzyme electrophoresis provides limited resolution of species relationships in the genus.     

Wing shape heritability and morphological divergence of the sibling species Drosophila mercatorum and Drosophila paranaensis

The fruit-flies Drosophila paranaensis and Drosophila mercatorum pararepleta are sibling species belonging to the repleta group. Females of these two species are normally considered to be morphologically indistinguishable while males only differ consistently in the morphology of their genitalia. These species are sympatric throughout a large area of their geographic distribution. In this study, we investigated the degree of morphological divergence between D. paranaensis and D. mercatorum pararepleta based on morphometric analysis of their wings. The ellipse method was used to describe the placement of the longitudinal and transversal wing veins as well as the size of the wing and the shape of its outline. The heritability under laboratory and field conditions was also estimated from the parameters generated. Multivariate analysis showed that wing morphology possessed sufficient differences to discriminate between the two species with a successful classification rate of 95-98% for females and 82-87% for males. The results of the autoclassification were confirmed by a cross-validation test for females (92-96%). Most measurements possessed significant natural heritability (a mean of 0.48 for D. mercatorum and 0.88 for D. paranaensis), indicating that the variation observed was related to differences in genes acting additively. The principal difference between the two species was in the placement of the posterior transverse wing vein. However, the pattern of morphological variation in the wings of both species was similar, possibly because of shared restrictions in wing development pathways.     

Ecological divergence among five co-occurring species of old-field goldenrods

Approximately 130 species of goldenrods are native to North America and many occur sympatrically. Such cooccurrence among closely related species raises the question of whether differences among the species in smallscale distribution and growth forms facilitate their co-occurrence. We investigated five goldenrods that frequently co-occur within their native ranges in Pennsylvania USA old fields. We measured goldenrod abundances, soil textures, nutrients, pH, and moisture within 30 old fields, and determined biomass allocation and flower and seed traits for each goldenrod species at a common site. Ordination revealed that Solidago altissima and S. gigantea were associated with fields having circum-neutral soils, whereas Euthamia graminifolia and S. rugosa achieved their highest abundances on acidic soils. Soil clay content and moisture may be associated with a further separation of species as the abundance of S. altissima tended to be higher on well-drained soils while S. gigantea had a tendency to attain its highest abundances on moist soils that had relatively stable moisture levels over time. Euthamia was more likely to be abundant on clay-rich soils while S. rugosa was often associated with soils containing little clay. Solidago juncea tended to associate with droughty soils that underwent marked soil-moisture changes over time. The latter goldenrod had the greatest absolute and relative root mass, the least absolute and relative leaf mass, highest seed-reproductive allocation, and heaviest achenes. In contrast, S. gigantea and Euthamia, which were often associated with more mesic and stable soil moisture conditions, allocated the least to roots and relatively high amounts of mass to leaves. Solidago gigantea, S. altissima, and Euthamia are invasive species across Europe. The species with the highest colonization rate across Europe, S. gigantea, allocated the most to reproduction in our study, while S. altissima, with the second highest colonization rate, was highly clonal producing the most rhizome mass. Life-history trait variation among goldenrods appears to be linked to differences in small-scale distributions and rates of colonization.     

Natural selection promotes divergence of transferrin among salmonid species

Transferrin is an iron-binding protein that plays an important role in iron metabolism and resistance to bacterial infection in a variety of organisms. A comparison of transferrin coding sequences from four salmonid species shows that the rate of evolution at nonsynonymous sites is significantly higher than the rate at synonymous sites, suggesting that positive natural selection for new alleles has played an important role in the evolution of transferrin in some salmon species. We hypothesize that the selective agent driving rapid divergence is interactions between host transferrin and the iron-scavenging proteins of pathogenic bacteria.     

Connecting recombination,nucleotide diversity,and species divergence in Drosophila

The association between recombination rate and nucleotide diversity provides compelling evidence for the action of natural selection across much of the Drosophila melanogaster genome. This conclusion is further supported by the lack of association between recombination rate and nucleotide divergence between species. However, studies of other species, including other Drosophila, have not always yielded the same results. Our recent study measured these parameters within the D. pseudoobscura species group using next-generation sequencing and high-throughput genotyping technologies. We documented fine-scale variation in crossover rate within D. pseudoobscura, and we observed that crossover variation was strongly associated with nucleotide diversity only when measured at a fine-scale. We also observed associations between crossover rate and sequence differences between D. pseudoobscura and its close relatives. These latter associations could have been driven in part by mutagenic effects associated with double-strand break repair, but we cannot exclude the possibility that it results primarily from shared ancestral polymorphisms. Overall, this work strongly underscores the importance of scale in testing for associations of recombination rate with other parameters, and it brings us one small step closer to understanding the role of natural selection and other evolutionary forces in shaping divergence among genomes.     

Rapid divergence and convergence of life‐history in experimentally evolved Drosophila melanogaster

Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life‐history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought.     

DNA barcode divergence among species and genera of birds and fishes

COI DNA barcoding is increasingly recognized as a significant new tool for the recognition and identification of animal species. Here, publicly available barcode data are compiled and analysed for birds (657 species) and fishes (1088 species). The proportion of species that cannot be barcode-distinguished by this marker is approximately 6.4% for birds and 2.1-2.5% for fishes. At all hierarchical taxonomic levels (species, genera, family, order, class), fish show greater mean COI divergence than birds. If two samples are barcode-identical, then for both birds and fishes, the probability that they are from the same species is 98-99%. The probability of conspecificity rapidly drops as divergence increases. At 2% COI divergence, this probability approximates to 1% for birds and 3% for fishes. The apparent difference between birds and fishes might partially reflect currently unrecognized cryptic species complexes in the latter. These probability estimates derive from pooled samples of birds and pooled samples of fishes, and will not apply in all situations. Recently evolved species complexes will have higher proportions of species that are barcode-identical. As barcode data accumulate, more refined statistical analyses will become possible.     

The population genetics of the origin and divergence of the Drosophila simulans complex species

The origins and divergence of Drosophila simulans and close relatives D. mauritiana and D. sechellia were examined using the patterns of DNA sequence variation found within and between species at 14 different genes. D. sechellia consistently revealed low levels of polymorphism, and genes from D. sechellia have accumulated mutations at a rate that is approximately 50% higher than the same genes from D. simulans. At synonymous sites, D. sechellia has experienced a significant excess of unpreferred codon substitutions. Together these observations suggest that D. sechellia has had a reduced effective population size for some time, and that it is accumulating slightly deleterious mutations as a result. D. simulans and D. mauritiana are both highly polymorphic and the two species share many polymorphisms, probably since the time of common ancestry. A simple isolation speciation model, with zero gene flow following incipient species separation, was fitted to both the simulans/mauritiana divergence and the simulans/sechellia divergence. In both cases the model fit the data quite well, and the analyses revealed little evidence of gene flow between the species. The exception is one gene copy at one locus in D. sechellia, which closely resembled other D. simulans sequences. The overall picture is of two allopatric speciation events that occurred quite near one another in time.     

Causes of variation in wing loading among Drosophila species

We examined influences on wing and body size in 11 species (12 strains) of Drosophila. Six measures of wing length and width were closely correlated with wing area and suggested little variation in wing shape among the species. Among ten species wing loading, an important factor in flight costs and manoeuvrability, increased as body mass increased at a rate consistent with expectations from allometric scaling of wing area and body mass to body length. Intraspecific variation in wing loading showed similar relationships to body mass. Density and temperature during larval development influenced wing loading through general allometric relations of body size and wing area. Temperature during the pupal stage, but not during wing hardening after eclosion, influenced wing area independently of body size. Wing area increased as growth temperature decreased. Individuals reared at cooler temperatures thus compensated for a potential allometric increase in wing loading by differentially enlarging the wing area during pupal development.     

Variable strength of translational selection among 12 Drosophila species

Codon usage bias in Drosophila melanogaster genes has been attributed to negative selection of those codons whose cellular tRNA abundance restricts rates of mRNA translation. Previous studies, which involved limited numbers of genes, can now be compared against analyses of the entire gene complements of 12 Drosophila species whose genome sequences have become available. Using large numbers (6138) of orthologs represented in all 12 species, we establish that the codon preferences of more closely related species are better correlated. Differences between codon usage biases are attributed, in part, to changes in mutational biases. These biases are apparent from the strong correlation (r = 0.92, P < 0.001) among these genomes' intronic G + C contents and exonic G + C contents at degenerate third codon positions. To perform a cross-species comparison of selection on codon usage, while accounting for changes in mutational biases, we calibrated each genome in turn using the codon usage bias indices of highly expressed ribosomal protein genes. The strength of translational selection was predicted to have varied between species largely according to their phylogeny, with the D. melanogaster group species exhibiting the strongest degree of selection.     

Rapid evolution of the sex-determining gene,transformer: structural diversity and rate heterogeneity among sibling species of Drosophila

While developmentally regulated genes are generally conserved, transformer (tra), a key locus involved in the regulation of sexual differentiation, is highly diverged between species of Drosophila. With an aim to understand its divergence between sibling species, we investigated tra sequence variation among members of the Drosophila melanogaster species complex, D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. In this species group, tra divergence is rapid yet clocklike and exhibits large differences in protein size. D. melanogaster contains a 13-amino acid tandem duplication, whereas D. sechellia possesses a 72-amino acid tandem duplication representing a 30% increase in total amino acid residues. We also found evidence of a nonrandom distribution of replacement substitutions and heterogeneity in substitution rates using clustering statistics and a codon substitution model. We show that tra's rapid divergence in this species complex is the result of generally lower selective constraints around regions that encode arginine-serine (RS) domains and a significantly higher rate of substitutions around the insertion site of D. sechellia's large duplication. The proximity of rapidly diverged regions to sites of nucleotide insertion suggests that higher local rates of mutation may provide a causal mechanism for TRA's rapid divergence in this subgroup. A comparison of tra orthologs across the genus Drosophila suggest that TRA maintains an assortment of RS domains for proper sex determining function while much of the protein evolves relatively unconstrained.     

Rapid evolution of courtship song pattern in Drosophila willistoni sibling species

Courtship behaviours may provide a more reliable means of identifying reproductively isolated taxa than traits such as morphology or many genetic markers. Here we describe the courtship songs of the Drosophila willistoni sibling species group, which consists of several species and subspecies. We find that song pattern is species-specific, despite significant differences among strains within species. D. paulistorum has the most variable song pattern, which reflects this species' traditional subdivision into semispecies. All the other species could be unambiguously identified by song. The major differences among these species was in the interpulse interval, as has been found in other studies of fly song. However, the interpulse intervals of the species studied here were often multimodal. This was partly due to the presence of multiple song types within the courtship repertoire, but it also reflected changes in interpulse interval within a song type by some males. Unusually, some species had distinctively patterned variation in interpulse interval. Song must have evolved rapidly within the species complex, probably due to sexual selection.     

Nucleotide divergence of the rp49 gene region between Drosophila melanogaster and two species of the Obscura group of Drosophila

Summary A 2.1-kb SStI fragment including the rp49 gene and the 3 end of the -serendipity gene has been cloned and sequenced in Drosophila pseudoobscura. rp49 maps at region 62 on the tip of chromosome II of this species. Both the coding and flanking regions have been aligned and compared with those of D. subobscura. There is no evidence for heterogeneity in the rate of silent substitution between the rp49 coding region and the rate of substitutions in flanking regions, the overall silent divergence per site being 0.19. Noncoding regions also differ between both species by different insertions/deletions, some of which are related to repeated sequences. The rp49 region of D. pseudoobscura shows a strong codon bias similar to those of D. subobscura and D. melanogaster. Comparison of the rates of silent (K _S ) and nonsilent (K _a ) substitutions of the rp49 gene and other genes completely sequenced in D. pseudoobscura and D. melanogaster confirms previous results indicating that rp49 is evolving slowly both at silent and nonsilent sites. According to the data for the rp49 region, D. pseudoobscura and D. subobscura lineages would have diverged some 9 Myr ago, if one assumes a divergence time of 30 Myr for the melanogaster and obscura groups.Offprint requests to: C. Segarra     

Body size vs abundance among parasite species: positive relationships?

Across species, abundance usually correlates negatively with body size. This intuitive pattern may result from size-dependent resource requirements in habitats where only finite amounts of resources are available. Among parasite species, it is possible that some resource limitations arc less severe than for free-living animals although this may depend on the type of parasites. The interspecific relationship between body size and abundance (measured as prevalence and intensity of infection) among parasites was tested in two groups of parasites. Among helminth endoparasites of fish, parasite body size correlated positively with prevalence and negatively with intensity of infection. Among copepod ectoparasites of fish, body size correlated positively with both prevalence and intensity. These trends were observed after controlling for the confounding influences of phylogeny and sampling effort. These contrasting patterns may result from the more intense link between body size and intensity-dependent regulation in endoparasites than in ectoparasites. The results of this comparative analysis suggest that parasite body size could be an important factor determining aspects of parasite abundance and distribution, including aggregation.