Juvenile hormone synthesis as related to egg development in neotenic reproductives of the termite Reticulitermes flavipes, with observations on urates in the fat body

The relationship between juvenile hormone (JH) synthesis and egg development, which is well documented in cockroaches, is much less studied in their close relatives, the termites. In this study of neotenic reproductives of the subterranean termite Reticulitermes flavipes, in vitro rates of juvenile hormone (JH) synthesis by corpora allata (CA) are related to vitellogenic egg development and the size of CA. The first study compared brachypterous and apterous neotenics in their first cycle of egg development and a second study compared physogastric and non-physogastric brachypterous and apterous neotenics. In both studies, rates of JH synthesis correlated with the size of CA as indicated by their length. Unlike the cockroach in which all basal oocytes are in the same stage of development, those in termites are in various stages. In brachypterous and apterous in the first cycle of egg development, CA with high rates of JH synthesis were from females with early vitellogenic basal oocytes, whereas CA with low rates of JH synthesis were from females with either pre-vitellogenic or mature basal oocytes. This pattern of JH synthesis is similar to the cycle of JH synthesis correlated with oocyte development in several cockroach species. In later oocyte maturations, CA from physogastric apterous females with ovaries containing mature, as well as growing oocytes, showed a wide range of JH production; the CA with the highest rates of JH synthesis were from females with the highest proportion of early vitellogenic oocytes suggesting that both mature and early vitellogenic oocytes interact to regulate JH synthesis. Rates of JH synthesis were related to the number of vitellogenic ovarioles. Physogastric brachypterous neotenics, compared to the other classes of neotenic females, had CA with 2- to 4-fold higher rates of JH synthesis and ovaries with 2.5- to 8-fold greater number of vitellogenic ovarioles. However, both physogastric brachypterous and apterous neotenics had more vitellogenic basal oocytes and less urate in their fat bodies than the respective non-physogastric neotenics. These results demonstrate the similarities and differences between the classes of neotenic termites and between reproductive females in cockroaches and termites.     

A primitive Late Pliocene cheetah, and evolution of the cheetah lineage

The cheetah lineage is a group of large, slender, and long-limbed cats with a distinctive skull and dental morphology, of which only the extant cheetah (Acinonyx jubatus) is present today. The lineage is characterized by having abbreviated, tall, and domed crania, and a trenchant dentition with a much reduced, posteriorly placed protocone on the upper carnassial. In this article, we report on a new discovery of a Late Pliocene specimen from China with an estimated age of ≈2.2–2.5 million years, making it one of the oldest specimens known to date. A cladistic analysis confirmed that it is the most primitive cheetah known, and it shares a number of unambiguous derived cranial traits with the Acinonyx lineage, but has more primitive dentition than previously known cheetahs, demonstrating that the many unusual skull and dental characters hitherto considered characteristic of cheetahs evolved in a gradual fashion. Isolated teeth of primitive cheetahs may not be recognizable as such, but can be confused with, for instance, those of leopards or other similar-sized pantherine cats or pumas. The age and morphology of the new specimen supports an Old World origin of the cheetah lineage, not a New World one, as has been suggested. We name the new species Acinonyx kurteni in honor of the late Björn Kurtén.     

Evolution of host range in Coleosporium ipomoeae,a plant pathogen with multiple hosts

Plants and their pathogens coevolve locally. Previous investigations of one host–one pathogen systems have demonstrated that natural selection favors pathogen genotypes that are virulent on a broad range of host genotypes. In the present study, we examine a system consisting of one pathogen species that infects three host species in the morning glory genus Ipomoea. We show that many pathogen genotypes can infect two or three of the host species when tested on plants from nonlocal communities. By contrast, pathogen genotypes are highly host-specific, infecting only one host species, when tested on host species from the local community. This pattern indicates that within-community evolution narrows the host breadth of pathogen genotypes. Possible evolutionary mechanisms include direct selection for narrow host breadth due to costs of virulence and evolution of ipomoea resistance in the host species.Much of plant-pathogen coevolution is mediated by “gene-for-gene” (GFG) interactions. These interactions involve R genes in plants and corresponding virulence/avirulence genes in the pathogen (1). At a given pair of corresponding loci, a host may carry either a resistant (Res) or a susceptible (Sus) allele, or both, with Res typically being dominant. The pathogen may carry either a virulent (Vir) allele or an avirulent (Avr) allele. Infection results, unless at one pair of corresponding loci, the plant R locus has a Res allele and the pathogen has the Avr allele. Models of the evolution of GFG systems generally predict that generalist pathogens (those able to infect multiple host-resistance genotypes) will be favored by natural selection over highly specialized genotypes that can infect only one resistance genotype (2–6). Experimental analyses of pathogen host breadth in natural plant–pathogen systems are consistent with these expectations in that pathogen isolates are generally able to infect multiple host-resistance genotypes, especially in host populations with high levels of resistance (7–10).With very few exceptions (11, 12), the evolution of pathogen host range has been examined, both theoretically and empirically, for a single pathogen species interacting with a single host species. Many pathogens, however, are capable of infecting multiple host species. Predictions of evolutionary models based on a single evolving host species cannot be clearly extrapolated to this situation. Moreover, there are reasons to believe that, with multiple host species, selection for generalism may not be as prevalent. Maintaining infectivity on multiple hosts requires continued success in the coevolutionary arms race with more than one independently evolving host genome. The conditions under which this maintained infectivity can occur are likely more restrictive than with only one host, although this possibility has not been examined theoretically. In addition, selection to maintain infectivity on a particular host is likely weaker when the pathogen population can successfully reproduce on another host (see ref. 13 for an analogous argument with respect to partial resistance). Finally, costs associated with the ability to infect multiple host species (e.g., ref. 14) are likely greater than costs associated with the ability to infect multiple genotypes within the same host. All of these factors would tend to weaken selection for a broad host range and thus promote the evolution of specialist pathogen genotypes within populations.One approach to determining whether there is an evolutionary tendency for host breadth to be narrowed within populations is to compare pathogen host breadth in its local native community with host breadth on hosts from outside its native community (e.g., refs. 9 and 13). The latter constitutes an estimate of host breadth on host species with which the pathogen has presumably not recently coevolved and is also an estimate of host breadth for a pathogen strain that has recently immigrated into a new community. If evolutionary processes within local communities act to promote specialization, host breadth should be lower on hosts from the native community. In this report, we demonstrate that this pattern is exhibited for a host–pathogen system consisting of one pathogen and three host species.     

From the Cover: Stem cells are units of natural selection for tissue formation,for germline development,and in cancer development

It is obvious that natural selection operates at the level of individuals and collections of individuals. Nearly two decades ago we showed that in multi-individual colonies of protochordate colonial tunicates sharing a blood circulation, there exists an exchange of somatic stem cells and germline stem cells, resulting in somatic chimeras and stem cell competitions for gonadal niches. Stem cells are unlike other cells in the body in that they alone self-renew, so that they form clones that are perpetuated for the life of the organism. Stem cell competitions have allowed the emergence of competitive somatic and germline stem cell clones. Highly successful germline stem cells usually outcompete less successful competitors both in the gonads of the genotype partner from which they arise and in the gonads of the natural parabiotic partners. Therefore, natural selection also operates at the level of germline stem cell clones. In the colonial tunicate Botryllus schlosseri the formation of natural parabionts is prevented by a single-locus highly polymorphic histocompatibility gene called Botryllus histocompatibility factor. This limits germline stem cell predation to kin, as the locus has hundreds of alleles. We show that in mice germline stem cells compete for gonad niches, and in mice and humans, blood-forming stem cells also compete for bone marrow niches. We show that the clonal progression from blood-forming stem cells to acute leukemias by successive genetic and epigenetic events in blood stem cells also involves competition and selection between clones and propose that this is a general theme in cancer.     

Histone H3-variant Cse4-induced positive DNA supercoiling in the yeast plasmid has implications for a plasmid origin of a chromosome centromere

The Saccharomyces cerevisiae 2-μm plasmid is a multicopy selfish genome that resides in the nucleus. The genetic organization of the plasmid is optimized for stable, high-copy propagation in host-cell populations. The plasmid's partitioning system poaches host factors, including the centromere-specific histone H3-variant Cse4 and the cohesin complex, enabling replicated plasmid copies to segregate equally in a chromosome-coupled fashion. We have characterized the in vivo chromatin topology of the plasmid partitioning locus STB in its Cse4-associated and Cse4-nonassociated states. We find that the occupancy of Cse4 at STB induces positive DNA supercoiling, with a linking difference (ΔLk) contribution estimated between +1 and +2 units. One plausible explanation for this contrary topology is the presence of a specialized Cse4-containing nucleosome with a right-handed DNA writhe at a functional STB, contrasted by a standard histone H3-containing nucleosome with a left-handed DNA writhe at a nonfunctional STB. The similarities between STB and centromere in their nucleosome signature and DNA topology would be consistent with the potential origin of the unusual point centromere of budding yeast chromosomes from the partitioning locus of an ancestral plasmid.     

Benefits of cooperation with genetic kin in a subsocial spider

Interaction within groups exploiting a common resource may be prone to cheating by selfish actions that result in disadvantages for all members of the group, including the selfish individuals. Kin selection is one mechanism by which such dilemmas can be resolved This is because selfish acts toward relatives include the cost of lowering indirect fitness benefits that could otherwise be achieved through the propagation of shared genes. Kin selection theory has been proved to be of general importance for the origin of cooperative behaviors, but other driving forces, such as direct fitness benefits, can also promote helping behavior in many cooperatively breeding taxa. Investigating transitional systems is therefore particularly suitable for understanding the influence of kin selection on the initial spread of cooperative behaviors. Here we investigated the role of kinship in cooperative feeding. We used a cross-fostering design to control for genetic relatedness and group membership. Our study animal was the periodic social spider Stegodyphus lineatus, a transitional species that belongs to a genus containing both permanent social and periodic social species. In S. lineatus, the young cooperate in prey capture and feed communally. We provide clear experimental evidence for net benefits of cooperating with kin. Genetic relatedness within groups and not association with familiar individuals directly improved feeding efficiency and growth rates, demonstrating a positive effect of kin cooperation. Hence, in communally feeding spiders, nepotism favors group retention and reduces the conflict between selfish interests and the interests of the group.     

Mutations in topoisomerase I as a self-resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants

Plants produce a variety of toxic compounds, which are often used as anticancer drugs. The self-resistance mechanism to these toxic metabolites in the producing plants, however, remains unclear. The plant-derived anticancer alkaloid camptothecin (CPT) induces cell death by targeting DNA topoisomerase I (Top1), the enzyme that catalyzes changes in DNA topology. We found that CPT-producing plants, including Camptotheca acuminata, Ophiorrhiza pumila, and Ophiorrhiza liukiuensis, have Top1s with point mutations that confer resistance to CPT, suggesting the effect of an endogenous toxic metabolite on the evolution of the target cellular component. Three amino acid substitutions that contribute to CPT resistance were identified: Asn421Lys, Leu530Ile, and Asn722Ser (numbered according to human Top1). The substitution at position 722 is identical to that found in CPT-resistant human cancer cells. The other mutations have not been found to date in CPT-resistant human cancer cells; this predicts the possibility of occurrence of these mutations in CPT-resistant human cancer patients in the future. Furthermore, comparative analysis of Top1s of CPT-producing and nonproducing plants suggested that the former were partially primed for CPT resistance before CPT biosynthesis evolved. Our results demonstrate the molecular mechanism of self-resistance to endogenously produced toxic compounds and the possibility of adaptive coevolution between the CPT production system and its target Top1 in the producing plants.     

INAUGURAL ARTICLE by a Recently Elected Academy Member:Causes of natural variation in fitness: Evidence from studies of Drosophila populations

DNA sequencing has revealed high levels of variability within most species. Statistical methods based on population genetics theory have been applied to the resulting data and suggest that most mutations affecting functionally important sequences are deleterious but subject to very weak selection. Quantitative genetic studies have provided information on the extent of genetic variation within populations in traits related to fitness and the rate at which variability in these traits arises by mutation. This paper attempts to combine the available information from applications of the two approaches to populations of the fruitfly Drosophila in order to estimate some important parameters of genetic variation, using a simple population genetics model of mutational effects on fitness components. Analyses based on this model suggest the existence of a class of mutations with much larger fitness effects than those inferred from sequence variability and that contribute most of the standing variation in fitness within a population caused by the input of mildly deleterious mutations. However, deleterious mutations explain only part of this standing variation, and other processes such as balancing selection appear to make a large contribution to genetic variation in fitness components in Drosophila.Advances in DNA sequencing methods have enabled geneticists to measure the amount of genetic variability in natural populations at the most basic level: the frequencies of variants in nucleotide sequences. This achievement has ended one component of a debate on the extent and causes of genetic variability that was initiated in the 1950s by Hermann Muller and Theodosius Dobzhansky (1, 2); we now know that DNA sequences are highly variable within the populations of most species (3). It has, however, been much harder to provide a definitive answer to the other component of this debate, which concerns the nature and intensity of the evolutionary forces that influence the frequencies of genetic variants within populations (1, 2, 4, 5). Are these variants mostly selectively neutral (6), with the fates of new mutations determined by random fluctuations in their frequencies (genetic drift)? Is selection on variants that affect fitness mostly purifying, so that mutations with harmful effects are rapidly removed from the population (1)? Or do many loci have variants maintained by balancing selection (2)? What fraction of newly arisen variants cause higher fitness and are in the process of spreading through the population and replacing their alternatives? How strong is the selection acting on nonneutral variants, and how much variation in fitness among individuals within populations is contributed by such variants? Does the existence of wide variation in fitness among individuals imply a genetic load that threatens the survival of the species (1)?These questions are very broad, and this paper deals only with one aspect of them. It focuses on the question of how recent inferences concerning the strength of purifying selection, derived from genome-wide surveys of DNA sequence variability, can be connected with the results of statistical studies of genetic variation in components of Darwinian fitness such as viability and fertility. I will refer to these two approaches as population genomics and quantitative genetics, respectively. The first approach sheds light on the general nature of the fitness effects of the DNA sequence variants found in natural populations, but says little about how these fitness effects are caused. The second tells us how much genetic variability exists for fitness traits, the rate at which it arise by mutation and something about the type of selection involved, but is silent about the nature of the underlying sequence variants.Surprisingly little attention has been paid to integrating these two lines of inquiry, except for ref. 7. I largely confine myself to results from studies of the fruitfly Drosophila, because this has been the most useful model organism for investigating these problems, especially by quantitative genetics methods. Current information derived from population genomics studies will first be reviewed, followed by an analysis of the results of quantitative genetics experiments on both mutational and standing variation. I show that the quantitative genetics results can only be explained if there is a significant input of new mutations with much larger effects on fitness than those inferred from population genomics. There also appears to be too much genetic variation in fitness components in natural populations to be explained purely by mutation selection balance, so that additional processes such as balancing selection must make an important contribution.     

Competitive release and facilitation of drug-resistant parasites after therapeutic chemotherapy in a rodent malaria model

Malaria infections frequently consist of mixtures of drug-resistant and drug-sensitive parasites. If crowding occurs, where clonal population densities are suppressed by the presence of coinfecting clones, removal of susceptible clones by drug treatment could allow resistant clones to expand into the newly vacated niche space within a host. Theoretical models show that, if such competitive release occurs, it can be a potent contributor to the strength of selection, greatly accelerating the rate at which resistance spreads in a population. A variety of correlational field data suggest that competitive release could occur in human malaria populations, but direct evidence cannot be ethically obtained from human infections. Here we show competitive release after pyrimethamine curative chemotherapy of acute infections of the rodent malaria Plasmodium chabaudi in laboratory mice. The expansion of resistant parasite numbers after treatment resulted in enhanced transmission-stage densities. After the elimination or near-elimination of sensitive parasites, the number of resistant parasites increased beyond that achieved when a competitor had never been present. Thus, a substantial competitive release occurred, markedly elevating the fitness advantages of drug resistance above those arising from survival alone. This finding may explain the rapid spread of drug resistance and the subsequently brief useful lifespans of some antimalarial drugs. In a second experiment, where subcurative chemotherapy was administered, the resistant clone was only partly released from competitive suppression and experienced a restriction in the size of its expansion after treatment. This finding raises the prospect of harnessing in-host ecology to slow the spread of drug resistance.     

Reproductive mode plasticity: aquatic and terrestrial oviposition in a treefrog

Diversification of reproductive mode is a major theme in animal evolution. Vertebrate reproduction began in water, and terrestrial eggs evolved multiple times in fishes and amphibians and in the amniote ancestor. Because oxygen uptake from water conflicts with water retention in air, egg adaptations to one environment typically preclude development in the other. Few animals have variable reproductive modes, and no vertebrates are known to lay eggs both in water and on land. We report phenotypic plasticity of reproduction with aquatic and terrestrial egg deposition by a frog. The treefrog Dendropsophus ebraccatus, known to lay eggs terrestrially, also lays eggs in water, both at the surface and fully submerged, and chooses its reproductive mode based on the shade above a pond. Under unshaded conditions, in a disturbed habitat and in experimental mesocosms, these frogs lay most of their egg masses aquatically. The same pairs also can lay eggs terrestrially, on vegetation over water, even during a single night. Eggs can survive in both aquatic and terrestrial environments, and variable mortality risks in each may make oviposition plasticity adaptive. Phylogenetically, D. ebraccatus branches from the basal node in a clade of terrestrially breeding species, nested within a larger lineage of aquatic-breeding frogs. Reproductive plasticity in D. ebraccatus may represent a retained ancestral state intermediate in the evolution of terrestrial reproduction.     

Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis

As paleopolyploid genomes evolve, the expression profiles of retained gene pairs are expected to diverge. To examine this divergence process on a large scale in a vertebrate system, we compare Xenopus laevis, which has retained approximately 40% of loci in duplicate after a recent whole-genome duplication (WGD), with its unduplicated relative Silurana (Xenopus) tropicalis. This comparison of ingroup pairs to an outgroup allows the direction of change in expression profiles to be inferred for a set of 1,300 X. laevis pairs, relative to their single orthologs in S. tropicalis, across 11 tissues. We identify 68 pairs in which X. laevis is inferred to have undergone a significant reduction of expression in at least two tissues since WGD. Of these pairs, one-third show evidence of subfunctionalization, with decreases in the expression levels of different gene copies in two different tissues. Surprisingly, we find that genes with slow rates of evolution are particularly prone to subfunctionalization, even when the tendency for highly expressed genes to evolve slowly is controlled for. We interpret this result to be an effect of allopolyploidization. We then compare the outcomes of this WGD with an independent one that happened in the teleost fish lineage. We find that if a gene pair was retained in duplicate in X. laevis, the orthologous pair is more likely to have been retained in duplicate in zebrafish, suggesting that similar factors, among them subfunctionalization, determined which gene pairs survived in duplicate after the two WGDs.     

Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants

Transposable elements, particularly LTR-retrotransposons, comprise the primary vehicle for genome size expansion in plants, while DNA removal through illegitimate recombination and intrastrand homologous recombination serve as the most important counteracting forces to plant genomic obesity. Despite extensive research, the relative impact of these opposing forces and hence the directionality of genome size change remains unknown. In Gossypium (cotton), the 3-fold genome size variation among diploids is due largely to copy number variation of the gypsy-like retrotransposon Gorge3. Here we combine comparative sequence analysis with a modeling approach to study the directionality of genome size change in Gossypium. We demonstrate that the rate of DNA removal in the smaller genomes is sufficient to reverse genome expansion through Gorge3 proliferation. These data indicate that rates of DNA loss can be highly variable even within a single plant genus, and that the known mechanisms of DNA loss can indeed reverse the march toward genomic obesity.     

Degenerate evolution of the hedgehog gene in a hemichordate lineage

The discovery of a set of highly conserved genes implicated in patterning during animal development represents one of the most striking findings from the field of evolutionary developmental biology. Existence of these “developmental toolkit” genes in diverse taxa, however, does not necessarily imply that they always perform the same functions. Here, we demonstrate functional evolution in a major toolkit gene. hedgehog (hh) encodes a protein that undergoes autocatalytic cleavage, releasing a signaling molecule involved in major developmental processes, notably neural patterning. We find that the hh gene of a colonial pterobranch hemichordate, Rhabdopleura compacta, is expressed in a dramatically different pattern to its ortholog in a harrimaniid enteropneust hemichordate, Saccoglossus kowalevskii. These represent two of the three major hemichordate lineages, the third being the indirect developing ptychoderid enteropneusts. We also show that the normally well-conserved amino acid sequence of the autoproteolytic cleavage site has a derived change in S. kowalevskii. Using ectopic expression in Drosophila, we find that this amino acid substitution reduces the efficiency of Hh autocatalytic cleavage and its signaling function. We conclude that the Hh sequence and expression in S. kowalevskii represent the derived state for deuterostomes, and we argue that functional evolution accompanied secondary reduction of the central nervous system in harrimaniids.     

Characterization of mononuclear phagocytic cells in medaka fish transgenic for a cxcr3a:gfp reporter

Chemokines and chemokine receptors are key evolutionary innovations of vertebrates. They are involved in morphogenetic processes and play an important role in the immune system. Based on an analysis of the chemokine receptor gene family in teleost genomes, and the expression patterns of chemokine receptor genes during embryogenesis and the wounding response in young larvae of Oryzias latipes, we identified the chemokine receptor cxcr3a as a marker of innate immune cells. Cells expressing cxcr3a were characterized in fish transgenic for a cxcr3a:gfp reporter. In embryos and larvae, cxcr3a-expressing cells are motile in healthy and damaged tissues, and phagocytic; the majority of these cells has the morphology of tissue macrophages, whereas a small fraction has a dendritic phenotype. In adults, cxcr3a-positive cells continue to specifically express myeloid-associate markers and genes related to antigen uptake and presentation. By light microscopy and ultrastructural analysis, the majority of cxcr3a-expressing cells has a dendritic phenotype, whereas the remainder resembles macrophage-like cells. After challenge of adult fish with bacteria or CpG oligonucleotides, phagocytosing cxcr3a-positive cells in the blood up-regulated il12p40 genes, compatible with their function as part of the mononuclear phagocytic system. Our results identify a marker of teleost mononuclear phagocytic cells and suggest a surprising degree of morphological and functional similarity between the innate immune systems of lower and higher vertebrates.