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PubMed2003

Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome.

The plant mitochondrial genome is complex in structure, owing to a high degree of recombination activity that subdivides the genome and increases genetic variation. The replication activity of various portions of the mitochondrial genome appears to be nonuniform, providing the plant with an ability to modulate its mitochondrial genotype during development. These and other interesting features of the plant mitochondrial genome suggest that adaptive changes have occurred in DNA maintenance and transmission that will provide insight into unique aspects of plant mitochondrial biology and mitochondrial-chloroplast coevolution. A search in the Arabidopsis genome for genes involved in the regulation of mitochondrial DNA metabolism revealed a region of chromosome III that is unusually rich in genes for mitochondrial DNA and RNA maintenance. An apparently similar genetic linkage was observed in the rice genome. Several of the genes identified within the chromosome III interval appear to target the plastid or to be targeted dually to the mitochondria and the plastid, suggesting that the process of endosymbiosis likely is accompanied by an intimate coevolution of these two organelles for their genome maintenance functions.

Amino Acid Sequence↗

PubMed2001

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

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

Animals↗

PubMed2001

Functional incompatibility between the fertilization systems of two allopatric populations of Callosobruchus maculatus (Coleoptera: Bruchidae).

Recent studies indicate that postcopulatory sexual selection may represent an important component of the speciation process by initiating reproductive isolation via the evolutionary divergence of fertilization systems. Using two geographically isolated populations of the polyandrous beetle Callosobruchus maculatus, we investigated divergence in fertilization systems by determining the extent of postcopulatory functional incompatibility. Through reciprocal, cross-population matings we were able to separately estimate the effects of male and female population origin and their interaction on the extent of last-male sperm precedence, female receptivity to further copulation and female oviposition. Our results indicate partial incompatibility between the fertilization systems of the two populations at all three functional levels. Males derived from the same population as females outcompete rival, allopatric males with respect to sperm preemption, sperm protection, and ability to stimulate female oviposition. This pattern is reciprocated in both populations indicating that postcopulatory, prezygotic events represent important mechanisms by which between-population gene flow is reduced. We suggest the partial gametic isolation observed is a by-product of the coevolution of male and female fertilization systems by a process of cryptic female choice. Our results are consistent with a mechanism akin to conventional mate choice models although they do not allow us to reject antagonistic sexual coevolution as the mechanism of cryptic female choice.

Animals↗

PubMed2002

Correlated evolution of male and female morphologles in water striders.

Sexually antagonistic coevolution may be an important force in the evolution of sexual dimorphism. We undertake a comparative study of correlated evolution of male and female morphologies in a clade of 15 water strider species in the genus Gerris (Heteroptera: Gerridae). Earlier studies have shown that superfluous matings impose costs on females, including increased energetic expenditure and predation risk, and females therefore resist males with premating struggles. Males of some species possess grasping structures and females of some species exhibit distinct antigrasping structures, which are used to further the interests of each sex during these premating struggles. We use this understanding, combined with coevolutionary theory, to derive a series of a priori predictions concerning both the types of traits in the two sexes that are expected to coevolve and the coevolutionary dynamics of these traits expected under sexually antagonistic coevolution. We then assess the actual pattern of correlated evolution in this clade with new morphometric methods combined with standard comparative techniques. The results were in agreement with the a priori predictions. The level of armament (different abdominal structures in the two sexes) was closely correlated between the sexes across species. Males are well adapted to grasping females in species in which females are well adapted to thwart harassing males and vice versa. Furthermore, our comparative analyses supports the prediction that correlated evolution of armament in the two sexes should be both rapid and bidirectional.

Animals↗

PubMed2003

Costs and benefits of evolving under experimentally enforced polyandry or monogamy.

Reproduction has classically been viewed as a predominantly cooperative process. However, over the last 20 years this concept has steadily yielded ground to one of continual conflict in which the interests of the sexes are typically discordant. Within this framework, males and females are seen to be locked into a perpetual arms race, each adaptation by one sex promoting the evolution of countermeasures in the other sex. However, under strict genetic monogamy, the interests of the sexes become congruent, and hence antagonistic coevolution does not occur. We subjected the fly Sepsis cynipsea, a species with conspicuous sexual conflict, to experimentally enforced monogamy or polyandry for 29 generations and evaluated the microevolutionary consequences. We found that there were longevity costs to females consistent with sexually antagonistic coevolution. However, our measure of female fitness, offspring emergence, did not differ between treatments, even though life-history characters such as fertility and fecundity did. Results are discussed in terms of costs and benefits of sexual selection and sexual conflict.

Animals↗

PubMed2004

A reconciliation analysis of host switching in plant-fungal symbioses.

Plant-fungal symbioses include many familiar antagonistic and mutualistic associations and some model cases of coevolution. The relationship between coevolution at the different evolutionary scales has remained an open question. Widespread host specificity and documented host switches offer conflicting indications of what to expect from comparisons of plant and fungal phylogenies. This study sought to establish the role of plant phylogeny in determining fungal phylogeny and the relative contributions of codivergence and host switching by comparing tree topologies for 15 plant-fungal symbioses. Second it attempted to characterize the relationship between phylogenetic congruence and switching. Trees were estimated from published sequences and reconciliation analysis was applied in the form of cophylogeny mapping using "jungles". This provided an exhaustive account of all possible switches capable of reconciling two associated phylogenies. A continuum of cophylogenetic dynamics was identified, ranging from mostly codivergence (e.g., Exobasidium) to mostly switching, (e.g., Erysiphe). Surprisingly, congruent solutions do not necessarily have fewer switches when using cophylogeny mapping, but a significant negative relationship between congruence and the distance of switches proved to be a useful indicator. According to reconciliation analysis, the contribution of host phylogeny varies widely across plant-fungal symbioses, making host specificity and coadaptation poor indicators of macroevolutionary trends because they are necessary, but not sufficient, conditions.

Computational Biology↗

PubMed2004

Genetic correlations and the coevolutionary dynamics of three-species systems.

The majority of species interact with at least several others. We develop simple genetic models of coevolution between three species where interactions are mediated by quantitative traits. We assume that one of the species has two quantitative traits, each of which governs its interaction with one of the other two species. We use this model to explore how genetic correlations between the two traits in the multivariate species shape the evolutionary dynamics and outcomes of three species interactions. Our results suggest that genetic correlations are most important when at least one of the interactions is between a predator and prey or parasite and host. In these cases, genetic correlations between traits lead to a wide variety of novel coevolutionary outcomes and dynamics. In particular, genetic correlations can affect the existence and stability of coevolutionary equilibrium points, and they can lead to recurrent or permanent maladaptation. When the three species interact only as competitors or mutualists, however, genetic correlations have no effect on the outcome of coevolution. In all cases, our results reveal the surprising conclusion that both positive and negative genetic correlations between traits have qualitatively identical effects on coevolutionary dynamics.

Alleles↗

PubMed1997

Relation between phylogeny of African green monkey CD4 genes and their respective simian immunodeficiency virus genes.

An apparent species-specific relatedness of SIVagm suggests a coevolution with their natural hosts. However, the exact species or subspecies classification of African green monkeys, AGM, is uncertain because current classification schemes rely on phenotype markers, while more definitive genetic data are lacking. In this study, the CD4 protein involved in tissue type recognition was genetically cloned and sequenced from PBMC RNA from all AGM species, including Barbados green monkeys (BGM). Phylogenetic trees were constructed that also included genomic CD4 nucleotide sequences from patas, sooty mangabeys, rhesus and pig-tail macaques, chimpanzees, and humans. Chimpanzees and humans consistently clustered together. Monkeys within the Cercopithecus genus formed a separate cluster which included pata monkeys, supporting its grouping as a member of Cercopithecus. Surprisingly, sooty mangabeys were genetically more closely related to Asian macaques than to other African species, which might explain why macaques are more susceptible to infection by the SIVsm group than to infection by SIVagm or HIV-1 and why patas, on the other hand, are highly susceptible to SIVagm infection. Based on CD4 genetic data, tantalus, vervets, grivets, and sabaeus formed separate subgroups with BGM grouping closely with vervets. The branching order of the AGM species was related to that of their respective SIVagm env sequences. The study suggests a strong correlation between CD4 phylogeny and the susceptibility of the host species to infection by a specific lentivirus and supports the assumption of a coevolution of SIVagm and AGM. CD4 sequencing is suggested as a relevant method for genetic determination of primate species.

Amino Acid Sequence↗

PubMed1990

Adding the heterochromatic YL arm to an X chromosome reduces reproductive fitnesses in Drosophila melanogaster: implications for the evolution of rDNA, heterochromatin, and reproductive isolation.

For X-Y exchange to be of importance in the coevolution of X and Y rDNA, there must be a mechanism to maintain cytologically normal X chromosomes in the face of continual infusions of X.YL chromosomes produced by X-Y exchanges. Replicated populations were founded with different frequencies of isogenic X and X.YL chromosomes. The X.YL chromosome declined in frequency over time in all lines. Relative fitnesses, estimated from chromosome frequency trajectories, were 0.40, 1.01, and 1.0 for X.YL/X.YL, X.YL/X, and X/X females and 0.75 and 1.0 for X.YL/Y and X/Y males, respectively. The equilibrium frequency for the X.YL chromosome due to the balance between X-Y exchange and selection was predicted to be 4-16 x 10(-4). The results strengthen the evidence for the involvement of X-Y exchange in the coevolution of X and Y rDNA arrays. Conditions for the evolution of reproductive isolation by sex-chromosome translocation are much less probable than previously supposed since the X.YL translocation chromosome is at a selective disadvantage to cytologically normal X chromosomes. Additional heterochromatin was not neutral but was only deleterious beyond a threshold, as one dose of the heterochromatic XL arm did not reduce female reproductive fitness, but two doses did.

Animals↗

PubMed2007

Insect/mammal associations: effects of Cuterebrid bot fly parasites on their hosts.

The effect of parasites on their hosts has implications for basic and applied ecology (e.g., species' population dynamics and distributions, biological control, and threats to at-risk species) and coevolution. Cuterebrid bot flies comprise one of the most-studied groups of insect parasites of mammals. Interest in their impact dates from at least 1857, when Cuterebra emasculator was so named because of the erroneous belief that its larvae castrate their hosts. This review addresses the effects of cuterebrid larvae on host biochemistry, physiology, behavior, and ecology. Despite high prevalence (peak values commonly range from 30% to 70%), at average intensities (one to three larvae per host) these parasites generally have little effect on the fitness or population dynamics of their typical hosts. This outcome likely reflects parasite/host coevolution favoring parasites that minimize harmful effects on hosts required for their survival and hosts that best tolerate perennial parasites they cannot avoid. In contrast, aggravated effects occur at higher intensities and with atypical hosts. Additional field studies involving experimental manipulation of infestation and spanning more than a few seasons are required to confirm these conclusions.

Animals↗

PubMed2006

Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs.

BACKGROUND: The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. RESULTS: We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the interspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. CONCLUSION: Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes.Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding their use as genetic markers.

Animals↗

PubMed2002

Genomic functional annotation using co-evolution profiles of gene clusters.

BACKGROUND: The current speed of sequencing already exceeds the capability of annotation, creating a potential bottleneck. A large proportion of the genes in microbial genomes remains uncharacterized. Here we propose a new method for functional annotation using the conservation patterns of gene clusters. If several gene clusters show the same coevolution pattern across different genomes it is reasonable to infer they are functionally related. The gene cluster phylogenetic profile integrates chromosomal proximity information and phylogenetic profile information and allows us to infer functional dependences between the gene clusters even at great distance on the chromosome. RESULTS: As a proof of concept, we applied our method to the genome of Escherichia coli K12 strain. Our method establishes functional relationships among 176 gene clusters, comprising 738 E. coli genes. The accuracy of pair phylogenetic profiles was compared with the single-gene phylogenetic profile and was shown to be higher. As a result, we are able to suggest functional roles for several previously unknown genes or unknown genomic regions in E. coli. We also examined the robustness of coevolution signals across a larger set of genomes and suggest a possible upper limit of accuracy for the phylogenetic profile methods. CONCLUSIONS: The higher-order phylogenetic profiles, such as the gene-pair phylogenetic profiles, can detect functional dependences that are missed by using conventional single-gene phylogenetic profile or the chromosomal proximity method only. We show that the gene-pair phylogenetic profile is more accurate than the single-gene phylogenetic profiles.

Alleles↗

PubMed2005

Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila.

Hybrids between species are often characterized by novel gene-expression patterns. A recent study on allele-specific gene expression in hybrids between species of Drosophila revealed cases in which cis- and trans-regulatory elements within species had coevolved in such a way that changes in cis-regulatory elements are compensated by changes in trans-regulatory elements. We hypothesized that such coevolution should often lead to gene misexpression in the hybrid. To test this hypothesis, we estimated allele-specific expression and overall expression levels for 31 genes in D. melanogaster, D. simulans, and their F1 hybrid. We found that 13 genes with cis-trans compensatory evolution are in fact misexpressed in the hybrid. These represent candidate genes whose dysregulation might be the consequence of coevolution of cis- and trans-regulatory elements within species. Using a mathematical model for the regulation of gene expression, we explored the conditions under which cis-trans compensatory evolution can lead to misexpression in interspecific hybrids.

Alleles↗

PubMed2006

Evolution under relaxed sexual conflict in the bulb mite Rhizoglyphus robini.

The experimental evolution under different levels of sexual conflict have been used to demonstrate antagonistic coevolution in muscids, but among other taxa a similar approach has not been employed. Here, we describe the results of 37 generations of evolution under either experimentally enforced monogamy or polygamy in the bulb mite Rhizoglyphus robini. Three replicates were maintained for each treatment. Monogamy makes male and female interests congruent; thus selection is expected to decrease harmfulness of males to their partners. Our results were consistent with this prediction in that females from monogamous lines achieved lower fecundity when housed with males from polygamous lines. Fecundity of polygamous females was not affected by mating system under which their partners evolved, which suggests that they were more resistant to male-induced harm. As predicted by the antagonistic coevolution hypothesis, the decrease in harmfulness of monogamous males was accompanied by a decline in reproductive competitiveness. In contrast, female fecundity and embryonic viability, which were not expected to be correlated with male harmfulness, did not differ between monogamous and polygamous lines. None of the fitness components assayed differed between individuals obtained from crosses between parents from the same line and those obtained from crosses between parents from different lines within the same mating system. This indicates that inbreeding depression did not confound our results. However, interpretation of our results is complicated by the fact that both males and females from monogamous lines evolved smaller body size compared to individuals from polygamous lines. Although a decrease in reproductive performance of males from monogamous lines was still significant when body size was taken into account, we were not able to separate the effects of male body size and mating system in their influence on fecundity of their female partners.

Animals↗

PubMedDate not supplied

The evolution of pathogenic trypanosomes.

In the absence of a fossil record, the evolution of protozoa has until recently largely remained a matter for speculation. However, advances in molecular methods and phylogenetic analysis are now allowing interpretation of the "history written in the genes". This review focuses on recent progress in reconstruction of trypanosome phylogeny based on molecular data from ribosomal RNA, the miniexon and protein-coding genes. Sufficient data have now been gathered to demonstrate unequivocally that trypanosomes are monophyletic; the phylogenetic trees derived can serve as a framework to reinterpret the biology, taxonomy and present day distribution of trypanosome species, providing insights into the coevolution of trypanosomes with their vertebrate hosts and vectors. Different methods of dating the divergence of trypanosome lineages give rise to radically different evolutionary scenarios and these are reviewed. In particular, the use of one such biogeographically based approach provides new insights into the coevolution of the pathogens, Trypanosoma brucei and Trypanosoma cruzi, with their human hosts and the history of the diseases with which they are associated.

Africa↗

PubMed2005

Unusually similar patterns of antibody V segment diversity in distantly related marsupials.

A pattern of coevolution between the V gene segments of Ig H and L chains has been noted previously by several investigators. Species with restricted germline V(H) diversity tend to have limited germline V(L) diversity, whereas species with high levels of germline V(H) diversity have more diverse V(L) gene segments. Evidence for a limited pool of V(H) but diverse V(L) gene segments in a South American opossum, Monodelphis domestica, is consistent with this marsupial being an exception to the pattern. To determine whether M. domestica is unique or the norm for marsupials, the V(H) and V(L) of an Australian possum, Trichosurus vulpecula, were characterized. The Ig repertoire in T. vulpecula is also derived from a restricted V(H) pool but a diverse V(L) pool. The V(L) gene segments of T. vulpecula are highly complex and contain lineages that predate the separation of marsupials and placental mammals. Thus, neither marsupial follows a pattern of coevolution of V(H) and V(L) gene segments observed in other mammals. Rather, marsupial V(H) and V(L) complexity appears to be evolving divergently, retaining diversity in V(L) perhaps to compensate for limited V(H) diversity. There is a high degree of similarity between the V(H) and V(L) in M. domestica and T. vulpecula, with the majority of V(L) families being shared between both species. All marsupial V(H) sequences isolated so far form a common clade of closely related sequences, and in contrast to the V(L) genes, the V(H) likely underwent a major loss of diversity early in marsupial evolution.

Animals↗

PubMed2005

Advertisement-call preferences in diploid-tetraploid treefrogs (Hyla chrysoscelis and Hyla versicolor): implications for mate choice and the evolution of communication systems.

Signals used for mate choice and receiver preferences are often assumed to coevolve in a lock-step fashion. However, sender-receiver coevolution can also be nonparallel: even if species differences in signals are mainly quantitative, females of some closely related species have qualitatively different preferences and underlying mechanisms. Two-alternative playback experiments using synthetic calls that differed in fine-scale temporal properties identified the receiver criteria in females of the treefrog Hyla chrysoscelis for comparison with female criteria in a cryptic tetraploid species (H. versicolor); detailed preference functions were also generated for both species based on natural patterns of variation in temporal properties. The species were similar in three respects: (1) pulses of constant frequency were as attractive as the frequency-modulated pulses typical of conspecific calls; (2) changes in preferences with temperature paralleled temperature-dependent changes in male calls; and (3) preference functions were unimodal, with weakly defined peaks estimated at values slightly higher than the estimated means in conspecific calls. There were also species differences: (1) preference function slopes were steeper in H. chrysoscelis than in H. versicolor; (2) preferences were more intensity independent in H. chrysoscelis than in H. versicolor; (3) a synergistic effect of differences in pulse rate and shape on preference strength occurred in H. versicolor but not in H. chrysoscelis; and (4) a preference for the pulse shape typical of conspecific calls was expressed at the species-typical pulse duration in H. versicolor but not in H. chrysoscelis. However, females of H. chrysoscelis did express a preference based on pulse shape when tested with longer-than-average pulses, suggesting a hypothesis that could account for some examples of nonparallel coevolution. Namely, preferences can be hidden or revealed depending on the direction of quantitative change in a signal property relative to the threshold for resolving differences in that property. The results of the experiments reported here also predict patterns of mate choice within and between contemporary populations. First, intraspecific mate choice in both species is expected to be strongly influenced by variation in temperature among calling males. Second, simultaneous differences in pulse rate and pulse shape are required for effective species discrimination by females of H. versicolor but not by females of H. chrysoscelis. Third, there is greater potential for sexual selection within populations and for discrimination against calls produced by males in other geographically remote populations in H. chrysoscelis than in H. versicolor.

Acoustic Stimulation↗

PubMed2002

[Phylogenetic analysis of intestinal bacterium using the distribution of intestinal bacterium in cyprinidate fishes and 16S DNA sequence data set].

There is a complex- and multi-effect for interdependent survival between intestinal- microorganisms and hosts. The symbiosis or coevolution that results from this effect for interdependent survival is used to reveal the phylogenies of hosts as well as intestinal microorganisms. The symbiosis or coevolution between intestinal microorganisms and hosts has been generated by interactive natural selection occurred between them. The symbiosis information that has been formed by interactive natural selection during a long evolutionary process must be recorded in DNA sequences. According to this point of view,we analyzed the phylogeny of 9 intestinal bacteria genera using their contents in intestines of 8 Cyrinidate species. At the same time,we fetched the 16S rRNA gene DNA sequences of 43 intestinal bacteria species being included in these nine genera of six intestinal families from GeneBank and constructed phylogenetic trees by NJ and MP methods. The NJ tree and MP tree have the same topologic configuration and are identical with the classical phylogenetic tree. Both the trees of 16S rRNA gene separated 43 bacteria species into gram-negative bacteria group and the gram-positive bacteria group,which are the first branches. Each of the first branches (groups) made again 6 subbranches (subgroups) where each subbranch is a family.Especially,the subbranch (subgroup) of enterobacteriaceace made again four small branches as genus taxon. This tree also shows that bacilliform bacterium is distinct from each other in the NJ and MP trees. After all species on the tree are merged,the topological configuration of the unrooted tree of 16S gene is closed to that of the host range unrooted tree.However,the position of bacillus is greatly changed on both the unrooted trees. The difference can be found if we increase the examination level and extend the hosts examed.

English Abstract↗