R-3 Repository :: Browsing by Author "Queller, David C."

Browsing by Author "Queller, David C."

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Amino Acid Repeats Cause Extraordinary Coding Sequence Variation in the Social Amoeba Dictyostelium discoideum
(Public Library of Science, 2012-09) Scala, Clea; Tian, Xiangjun; Mehdiabadi, Natasha J.; Smith, Margaret H.; Saxer, Gerda; Stephens, Katie; Buzombo, Prince; Strassmann, Joan E.; Queller, David C.
Protein sequences are normally the most conserved elements of genomes owing to purifying selection to maintain their functions. We document an extraordinary amount of within-species protein sequence variation in the model eukaryote Dictyostelium discoideum stemming from triplet DNA repeats coding for long strings of single amino acids. D. discoideum has a very large number of such strings, many of which are polyglutamine repeats, the same sequence that causes various human neurological disorders in humans, like Huntington's disease. We show here that D. discoideum coding repeat loci are highly variable among individuals, making D. discoideum a candidate for the most variable proteome. The coding repeat loci are not significantly less variable than similar non-coding triplet repeats. This pattern is consistent with these amino-acid repeats being largely non-functional sequences evolving primarily by mutation and drift.
Collective worker control in the African social wasp, Polybioides tabidus
(2000) Henshaw, Michael Thomas; Strassmann, Joan E.; Queller, David C.
Social insect workers often sacrifice their own reproduction so that they may help relatives to reproduce more successfully. However, genetically dissimilar colony-mates may prefer to aid different kin, and this may result in disruptive conflicts. I developed polymorphic microsatellite genetic loci for the African swarm-founding wasp Polybioides tabidus to examine mechanisms to reduce such conflicts. Swarm-founding wasps have many reproductive queens in their colonies which should lower relatedness, increasing the potential for conflicts. I found that even though P. tabidus colonies contained many queens, relatedness was elevated because new queens were only produced after the number of old queens had been reduced to one, or nearly one. Queens were thus highly related, elevating relatedness in the colony as a whole, and promoting sociality. This unique pattern of queen production is consistent with a worker manipulation of the sex ratios known as cyclical oligogyny. Under cyclical oligogyny, new queens are produced when the colony has few queens, while males are produced when the colony has many queens. The males were indeed produced when queen number was higher, and I found evidence that the workers collectively controlled male production. Colonies which produced normal haploid males also produced diploid males, which have a diploid genome but are homozygous at the sex determining locus. P. tabidus does not appear to effectively distinguish between diploid and haploid males, and diploid males should have occurred in colonies without haploid males too. Their absence indicates that they were actively eliminated from colonies in which the workers did not favor male production. Workers also may have controlled who produced the males. Each worker should prefer to produce the males herself. However, I found that the queens produced the males. This may be explained by collective worker policing because the workers would be more highly related to queen-derived males than to the sons of other workers and should prevent reproduction by other workers. Alternatively, each worker might restrain herself if worker reproduction was costly to the success of the colony. The results of this study indicate that collective worker control is an important mechanism stabilizing cooperation.
Computer simulations of kin selection
(1993) Goodnight, Keith Flewellen; Queller, David C.
The theory of kin selection is central to the understanding of social evolution. Recent theoretical work suggests a limitation on the action of kin selection in structured populations. The first such limit involves a specialized population structure, termed "budding viscosity," common to social insects, in which new groups are formed by fission with no individual dispersal. An argument based on the separation of kin selection dynamics into among and within group components suggests that kin selection cannot operate in this structure. However, stochastic computer simulations show that random variation among daughter groups can supply the needed among-groups variation and allow kin selection to proceed. The second limit on kin selection involves simple population viscosity, in which individuals disperse limited distances and so are related to their neighbors. Altruism toward neighbors, favored by kin selection, is opposed by local competition. Computer simulation confirms this limitation and shows that some form of specific kin recognition is required to favor the evolution of altruism by kin selection. All applications of kin selection require a measure of genetic relatedness; a computer program for calculating this statistic from genetic data on natural populations is described.
Conflict and cooperation in the tropical wasp, Parachartergus colobopterus, and the chimeric multicellular organism, Dictyostelium discoideum
(2003) Platt, Thomas Gene; Strassmann, Joan E.; Queller, David C.
Several transitions to higher levels of biological organization have punctuated the history of life. These transitions occur when cooperative alliances lead to the integration of non-identical partners into more complex wholes. Yet there is inevitable conflict within these cooperative alliances. In the following chapters I investigate reproductive conflicts of interest between cooperators within insect societies and chimeric multicellular organisms. In the first chapter I show that in the tropical wasp, Parachartergus colobopterus, workers use aggression toward totipotent, emerging females to influence the reproductive future of the latter. By doing this workers resolve conflict over who reproduces in accord with their collective interests. In the second chapter I show that environmental heterogeneity can affect the outcome of conflict between co-aggregating clonal lineages of Dictyostelium discoideum. This helps account for the coexistence of cheaters and victims in natural populations of D. discoideum.
Evolution of trinucleotide microsatellite sequence variation across the Polistinae, a social wasp subfamily
(1998) Zhu, Yong; Strassmann, Joan E.; Queller, David C.
I examined sequences of 3 microsatellite loci that were derived from Polistes bellicosus investigated their evolution in 78 species from four tribes in the Polistinae subfamily of wasps. I found that the basic repeat structure of the microsatellite repeat region at these three loci was conserved across species at the subgenus level. Besides changes in the number of repeats, base substitutions were the dominant mutations in the repeat regions. The tribe from which the loci were isolated had longer repeat regions and more perfect repeats that the tribes at the same loci. At microsatellite flanking regions, I found that a high proportion of insertions duplicated 1-4 bases of their preceding sequences. Microsatellite repeats may originate from these such little insertions.
Evolutionary conflict in chimeras of the social amoeba, Dictyostelium discoideum
(2002) Fortunato, Angelo; Strassmann, Joan E.; Queller, David C.
Molecular biologists have extensively studied Dictyostelium discoideum and consider it a model organism for the study of cellular differentiation but paradoxically many aspects of the natural life and evolution of this organism are unknown. My study demonstrates there is high clonal diversity in nature and that different clones coexist in the same small soil sample. Thus, amoebae with different genotypes can join in the same multicellular organism making a genetic chimera in nature. I also show that a linear dominance hierarchy describes the interactions of genetically distinct clones in competition for survival in the multicellular stage. In fact, during this stage the amoebae differentiate into different types of cells allowing the pseudoplasmodium to form a fruiting body consisting of two principle cell types: the spore and the stalk cells. The formation of the fruiting body probably guarantees a better survival and dispersion of the spore but requires the death of 20% of the cells that initially comprise the pseudoplasmodium that differentiate into the stalk and the basal disc. Contributions of two clones in a chimera to spore and stalk are often unequal, with one clone taking advantage of the other's stalk contribution. To assess whether there was a hierarchy of exploitation among clones, I competed all possible pairs among seven clones. I found a clear linear hierarchy with one clone being most dominant, and the bottom clone losing in competition to all the others. The hierarchy at an earlier stage, evaluated with prespore and prestalk cells in the slug, was not as clear. These results suggest that there is a single principal mechanism for differential contribution to the spore and that it involves more than spore/stalk competition. My results legitimate the use of chimeric D. discoideum as a model organism for the investigation of issues relating to coexistence and conflict between cells during organismal development and thus as a simple model for the relationship between social organisms.
Evolutionary costs and benefits of a newly discovered symbiosis between the social amoeba Dictyostelium and bacteria
(2012) Brock, Debra Lynn Adams; Strassmann, Joan E.; Queller, David C.
Recent work has shown that microorganisms are surprisingly like animals in having sophisticated behaviours such as cooperation, communication, and recognition, as well as many kinds of symbioses. Here we show first that the social amoeba Dictyostelium discoideum has a primitive farming symbiosis that includes dispersal and prudent harvesting of the crop. About one-third of wild-collected clones engage in husbandry of bacteria. Instead of consuming all bacteria in their patch, they stop feeding early and incorporate bacteria into their fruiting bodies. They then carry bacteria during spore dispersal and can seed a new food crop, which is a major advantage if edible bacteria are lacking at the new site. However, if they arrive at sites already containing appropriate bacteria, the costs of early feeding cessation are not compensated, which may account for the dichotomous nature of this farming symbiosis. We also observed farmer Dictyostelium discoideum clones carry bacteria that they do not use as food. We hypothesized that these bacteria may play a defensive role against other D. discoideum clones. In our second study, we investigated the impact of these bacteria-carrying farmers on non-farming D. discoideum clones. We found that the presence of farming clones reduces spore production in non-farmers. Furthermore, this effect increases with frequency of farming clones, demonstrating the vulnerability of non-farming clones to farmers though in this experiment we had not separated the effects of the farmer clone and the bacteria they carry. In our third study we exposed non-farmers to a filtered supernatant from the most common non-food carried bacterium, Burkholderia xenovorans . This supernatant is likely to carry whatever the bacteria are producing. We treated Dictyostelium clones at the beginning of the social stage and found that the supernatant enhanced spore production of farming clones and hurt spore production of non-farming clones. This study shows that the effects of the bacteria can be restricted to a filtered supernatant alone. This discovery of symbiosis of D. discoideum with bacteria, and its impact on social interactions among D. discoideum clones will provide a fertile ground for further experiments on the evolution of sociality.
Exploiting new terrain: An advantage to sociality in the slime mold Dictyostelium discoideum
(2006) Kuzdzal, Jennie J.; Strassmann, Joan E.; Queller, David C.
Identifying benefits to cooperation is important in studying social evolution. When the social amoebae of Dictyostelium discoideum starve, they aggregate to form multicellular slugs that migrate towards the soil surface to form fruiting bodies. Multicellularity in D. discoideum is thought to help provide protection from predators and aid in the dispersal of reproductive spores. Here we show an additional benefit of local dispersal. Utilizing D. discoideum's phototactic behavior, we induced slug migration over bacteria and show that this passage results in the removal of bacteria. Time-lapse video revealed that slugs do not dissociate on contact with bacteria, rather cells sloughed from the migrating slugs consume the prey and reproduce. Using an aggregation mutant, we show that the cells slugs shed are able to reach and colonize food sources solitary amoebae cannot. We propose that the exploitation of local food patches is an important selective benefit favoring multicellularity in D. discoideum .
Fitness consequences of genetic and phenotypic chimeras in the social amoeba, Dictyostelium discoideum
(2008) Castillo, David I.; Strassmann, Joan E.; Queller, David C.
Multicellular organisms regularly eliminate unfit or harmful cells in the process of normal development. This high level of cooperation is maintained because all cells within the organism are genetically identical and thus, have the same evolutionary interests. However, there are some multicellular organisms that develop not from a single cell but from many individuals. In the case of the social amoebae, Dictyostelium discoideum, the usually solitary amoebae aggregate with nearby cells when starving to form a motile, multicellular slug that migrates to the soil surface and forms a fruiting body consisting of a bail of spores held aloft by a stalk of dead cells. These aggregations may be a mix of genetically identical individuals or of multiple clones, called genetic chimeras. Within chimeras, a conflict may arise over which cells contribute to the reproductive spores versus the dead stalk. Previous work on D. discoideum has shown that uniclonal slugs migrate further than chimeric slugs of the same size across agar. Here we test whether this resuits in a fitness cost under more natural conditions. We examined migration of slugs across decaying leaves and soil as well as migration up through layers of these substrates, closely reflecting the natural migration of D. discoideum slugs in the wild. In most trials, chimeras performed worse than single clones. Thus, chimerism in D. discoideum should produce a fitness cost likely to be important in nature. Since D. discoideum readily mixes with multiple clones, the potential for conflict is high. Diverging evolutionary interests in chimeras could influence adaptive strategies for filling the spore and stalk roles. Here we explore the strategy for filling these roles in phenotypic chimeras, mixes of cells differing only in physical condition. We explore the fitness of D. discoideum spores and found that cells with better prospects tend to represent the subsequent generations. However, we also found that D. discoideum amoebae did not respond to the condition of cells with which they aggregate. Our results indicate that, within a genetically identical population, the differentiation of spore and stalk roles is a competition based on the condition of the individual cells.
Genetic structure of Polistes dominulus foundress associations
(1998) Zacchi, Francesca; Strassmann, Joan E.; Queller, David C.
Kin-selection theory states that individuals can increase their total fitness both through direct reproduction and through reproduction of relatives. The recently developed social contract theory asserts that dominant females should yield some direct reproduction to the subordinates in order to keep them in the colony. The theory predicts that a dominant will cede more reproduction to an unrelated subordinate than to a related subordinate since it will take more to keep her. I found that the social wasp, Polistes dominulus, is unusual in that foundresses regularly nest with non-relatives, even when relatives are available on other nests. This offers the opportunity to test one of the basic predictions of social contract theory, that reproductive skew increases as relatedness among co-foundresses increases. Subordinates of the collected colonies did get a small fraction of direct reproduction, but there was no difference in skew among colonies with different co-foundress relatednesses, contrary to skew theory predictions. Subordinates's relatedness to the queen does not affect colony efficiency. This study found no sign of either higher cooperation in colonies with more related females or greater conflicts in colonies founded by unrelated females.
Genotypic diversity and population structure in Dictyostelium discoideum
(2004) Smith, Margaret Harris; Strassmann, Joan E.; Queller, David C.
Current population genetics literature presumes a lack of population structure in microorganisms due to their large population sizes, ubiquitous dispersal, and absence of geographic barriers. Contrary to this, we found evidence of great population subdivision in the social amoeba, Dictyostelium discoideum. Pairwise values of Fst and Rst were significant between samples collected from sites separated by distances from 100m--10,000km (P < 0.05 after sequential Bonferroni). Three- and two-level analyses of molecular variance (AMOVA) confirmed the existence of population structure (Fst 0.30, Rst = 0.48, P < 0.001 for three-level; Fst = 0.297, Rst = 0.474, P < 0.001 for two-level). Further, linearized pairwise Fst values were significantly correlated with natural logarithm of geographic distance (r = 0.471, P < 0.012) indicating isolation by distance. Genotypic diversity of populations remained moderate (Nei (1987) average gene diversity ∼0.50) in spite of the decreased population diversity expected with such Fst and Rst values.
Kin discrimination and possible cryptic species in the social amoeba Polysphondylium violaceum
(BioMed Central, 2011) Kalla, Sara E.; Queller, David C.; Lasagni, Andrea; Strassmann, Joan E.
Abstract Background The genetic diversity of many protists is unknown. The differences that result from this diversity can be important in interactions among individuals. The social amoeba Polysphondylium violaceum, which is a member of the Dictyostelia, has a social stage where individual amoebae aggregate together to form a multicellular fruiting body with dead stalk cells and live spores. Individuals can either cooperate with amoebae from the same clone, or sort to form clonal fruiting bodies. In this study we look at genetic diversity in P. violaceum and at how this diversity impacts social behavior. Results The phylogeny of the ribosomal DNA sequence (17S to 5.8S region) shows that P. violaceum is made up of at least two groups. Mating compatibility is more common between clones from the same phylogenetic group, though matings between clones from different phylogenetic groups sometimes occurred. P. violaceum clones are more likely to form clonal fruiting bodies when they are mixed with clones from a different group than when they are mixed with a clone of the same group. Conclusion Both the phylogenetic and mating analyses suggest the possibility of cryptic species in P. violaceum. The level of divergence found within P. violaceum is comparable to the divergence between sibling species in other dictyostelids. Both major groups A/B and C/D/E/F show kin discrimination, which elevates relatedness within fruiting bodies but not to the level of clonality. The diminished cooperation in mixes between groups suggests that the level of genetic variation between individuals influences the extent of their cooperation.
Multilocus test for nuclear introgression between Macaca mulatta and M fascicularis: Evidence for gene flow in macaques
(2008) Stevison, Laurie Sherie; Kohn, Michael H.; Wiess, Olga K.; Weiss, Harry C.; Queller, David C.; Whitney, Ken; Kronforst, Marcus
Introgression due to hybridization is important for our understanding of species divergence. In this study, we analyze potential introgression between Macaca mulatta and M fascicularis using DNA sequences from 19 genes. While the putative introgression between these species has been studied previously, it has not been analyzed using nuclear loci from multiple chromosomes. Phylogenetic analyses of these genes revealed shared variation at several of the loci. Neutrality tests indicated balancing selection did not fully account for these shared polymorphisms. Testing the null model of Isolation with Migration (IM) indicated interspecific gene flow caused the shared variation, revealing significant gene flow from M mulatta into M fascicularis (2Nm=l.23) and very limited gene flow from M fascicularis into M mulatta (2Nm=0.07). This asyrtlmetry is consistent with previously reported differences in male aggression between these species. Genome-enabled detection of hybridization in these primates opens new avenues of research in genome evolution and speciation.
A new social gene in Dictyostelium discoideum, chtB
(2013) Santorelli, Lorenzo A.; Kuspa, Adam; Shaulsky, Gad; Queller, David C.; Strassmann, Joan E.; National Science Foundation; BioMed Central
Background: Competitive social interactions are ubiquitous in nature, but their genetic basis is difficult to determine. Much can be learned from single gene knockouts in a eukaryote microbe. The mutants can be competed with the parent to discern the social impact of that specific gene. Dictyostelium discoideum is a social amoeba that exhibits cooperative behavior in the construction of a multicellular fruiting body. It is a good model organism to study the genetic basis of cooperation since it has a sequenced genome and it is amenable to genetic manipulation. When two strains of D. discoideum are mixed, a cheater strain can exploit its social partner by differentiating more spore than its fair share relative to stalk cells. Cheater strains can be generated in the lab or found in the wild and genetic analyses have shown that cheating behavior can be achieved through many pathways. Results: We have characterized the knockout mutant chtB, which was isolated from a screen for cheater mutants that were also able to form normal fruiting bodies on their own. When mixed in equal proportions with parental strain cells, chtB mutants contributed almost 60% of the total number of spores. To do so, chtB cells inhibit wild type cells from becoming spores, as indicated by counts and by the wild type cells’ reduced expression of the prespore gene, cotB. We found no obvious fitness costs (morphology, doubling time in liquid medium, spore production, and germination efficiency) associated with the cheating ability of the chtB knockout. Conclusions: In this study we describe a new gene in D. discoideum, chtB, which when knocked out inhibits the parental strain from producing spores. Moreover, under lab conditions, we did not detect any fitness costs associated with this behavior.
Polymorphism of microsatellites in coding regions of Dictyostelium discoideum
(2005) Scala, Clea; Queller, David C.; Strassmann, Joan E.
Microsatellites are repetitive DNA sequences with high rate of slippage mutations, which cause changes in length. As expected by the neutral theory of molecular evolution the level of polymorphism of these sequences is high when located in non-coding regions that may experience little selection. We tested the hypothesis that triplet repeat microsatellites located in coding regions of the social amoeba Dictyostelium discoideum should have a low level of polymorphism, given the presumably stronger effect on fitness of changes in coding DNA. We analyzed the length of 8 microsatellites located in coding regions of Dictyostellium discoideum in 114 clones of the North America population, divided in 5 subpopulations. Our results showed that each of the eight loci was very highly variable in the population. The lowest range of length variation was 17 repeats (51 bp) for a microsatellite in the ATG1 gene and the maximum range was 78 repeats (234 bp) for a microsatellite in the dimA gene. We tested the possibility that the level of polymorphism was due to population structure. Although present, the population structure was low, and consequently not responsible for the high polymorphism.
Reproductive conflicts in the social wasp, Eustenogaster fraterna, and in the social amoeba, Dictyostelium discoideum
(2002) Landi, Monica; Strassmann, Joan E.; Queller, David C.
My dissertation encompasses three studies of social behavior. Two explore the reproductive conflicts that occur between cooperating individuals. I examine conflict at two levels: within colonies of the social wasp, Eustenogaster fraterna, and within chimeric multicellular organisms formed by the social amoeba, Dictyostelium discoideum. The third project investigates the occurrence of sexual reproduction in a natural population of D. discoideum. Eustenogaster fraterna belongs to the basal eusocial family of stenogastrine wasps. Colonies are small averaging only 2.7 adult females but only one mated female. I examined the reproductive and genetic structure of 18 colonies by genotyping all within-colony individuals and assessing the ovarian development of females. My results show that 85% of females were potential reproducers. Adult females were not related as full sisters. Some brood could not be assigned to any of the adult females, suggesting that subordinate females could inherit the nest and replace the dominant female. D. discoideum live as free-living, single cells, but when starved they aggregate to form a multicellular fruiting body. Genetically distinct clones of D. discoideum co-aggregate to form genetic chimeras. 20% of cells form the stalk of the fruiting body and die, while others become reproductive spores. One clone can exploit the other by contributing less than its proportional share to the sterile stalk. I investigated whether cheating is a strategy dependent on the relative proportion of the clones aggregating. In a chimera, a rare clone could benefit by avoiding forming the stalk because it is less related to the reproductive part. My results do not support the frequency-dependence strategy. I investigated the occurrence of sexual reproduction in a natural population of D. discoideum, using the approach of estimating linkage disequilibrium in the population at one site. My results show that recombination does occur and is due to sexual reproduction not to parasexuality. In sum, conflicts within societies can be mitigated. E. fraterna workers gain insurance advantages by obtaining indirect genetic benefits or inheritance of work force. D. discoideum clones gain cheating advantages either when rare or common in the aggregation. Recombination yields novel genotypes; this might increase the complexity of interactions between co-aggregating clones.
The origin of microsatellites and their application to the study of social evolution in the cellular slime mold, Dictyostelium discoideum
(2000) Zhu, Yong; Strassmann, Joan E.; Queller, David C.
Data from the Human Gene Mutation Database were used to contrast the alternative hypotheses that microsatellites arise through insertions or through substitutions. The results showed that a high percentage of small insertions created novel microsatellite repeats through the duplication of the adjacent sequences. However substitutions were still the dominant source of new microsatellites since they are so much more common than insertions. Although insertions contributed a minority of new repeat loci, their relative importance increased rapidly with repeat motif sizes. Microsatellite techniques were then applied to examine genetic conflicts in the cellular slime mold, Dictyostelium discoideum. Microsatellite genotyping showed that genetically distinct clones generally formed multicellular fruiting structures together in the mixing experiments. More interestingly, some clones were found to preferentially become reproductive spores instead of non-reproductive altruistic stalk cells. These conflicts of genetic interest make D. discoideum a potential excellent model system for social evolution.
Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum
(Public Library of Science, 2012) Saxer, Gerda; Havlak, Paul; Fox, Sara A.; Quance, Michael A.; Gupta, Shara; Fofanov, Yuriy; Strassmann, Joan E.; Queller, David C.
Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10(-9), with a Poisson confidence interval of 4.1×10(-9) - 9.5×10(-9), per nucleotide per generation is slightly lower than estimates for other taxa. The mutation rate estimate for the nuclear DNA of 2.9×10(-11), with a Poisson confidence interval ranging from 7.4×10(-13) to 1.6×10(-10), is the lowest reported for any eukaryote. These results are consistent with low microsatellite mutation rates previously observed in D. discoideum and low levels of genetic variation observed in wild D. discoideum populations. In addition, D. discoideum has been shown to be quite resistant to DNA damage, which suggests an efficient DNA-repair mechanism that could be an adaptation to life in soil and frequent exposure to intracellular and extracellular mutagenic compounds. The social aspect of the life cycle of D. discoideum and a large portion of the genome under relaxed selection during vegetative growth could also select for a low mutation rate. This hypothesis is supported by a significantly lower mutation rate per cell division in multicellular eukaryotes compared with unicellular eukaryotes.

Browsing by Author "Queller, David C."

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