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PubMed2004

Identification of allelic variants of the bovine immune regulatory molecule CEACAM1 implies a pathogen-driven evolution.

Carcinoembryonic antigen-related cell adhesion molecule (CEACAM1), the primordial member of the carcinoembryonic antigen (CEA) family, functions as a MHC-independent natural killer (NK) cell inhibitory receptor, regulates T and B cell proliferation, and induces dendritic cell (DC) maturation. Despite these fundamental functions, CEACAM1 and most of the CEA family members differ significantly in primates and rodents. A number of diverse murine and human pathogens use CEACAM1 as a cellular receptor, indicating that the observed species-specific differences are the result of divergent molecular pathogen/host coevolution. To gain deeper insight into its evolution and function, we cloned CEACAM1 cDNA from cattle as a representative of a third mammalian order. Bovine CEACAM1 differs considerably from rodent and primate CEACAM1 due to deletion of the B domain exon which was most likely caused by insertion of LINE/SINE sequences and reveals alternative splicing within the transmembrane exon. However, the characteristic long and short isoforms exist which contain or lack the typical immunoreceptor tyrosine-based inhibitory motifs (ITIM) in their cytoplasmic tails, respectively. Bovine peripheral blood lymphocytes (PBL) express only ITIM-containing CEACAM1 isoforms, and upregulate their expression upon stimulation, suggesting an inhibitory function in these cells. As found in rodents, two clearly distinct CEACAM1 alleles exist in cattle. In the a allele, a unique deletion of three amino acids is found in the N domain, which is important for pathogen binding in mice and humans. This is consistent with the notion that CEACAM1 serves or has served as a pathogen receptor in cattle.

Alleles↗

PubMed2005

Unusual structure of ribosomal DNA in the copepod Tigriopus californicus: intergenic spacer sequences lack internal subrepeats.

Eukaryotic nuclear ribosomal DNA (rDNA) is typically arranged as a series of tandem repeats coding for 18S, 5.8S, and 28S ribosomal RNAs. Transcription of rDNA repeats is initiated in the intergenic spacer (IGS) region upstream of the 18S gene. The IGS region itself typically consists of a set of subrepeats that function as transcriptional enhancers. Two important evolutionary forces have been proposed to act on the IGS region: first, selection may favor changes in the number of subrepeats that adaptively adjust rates of rDNA transcription, and second, coevolution of IGS sequence with RNA polymerase I transcription factors may lead to species specificity of the rDNA transcription machinery. To investigate the potential role of these forces on population differentiation and hybrid breakdown in the intertidal copepod Tigriopus californicus, we have characterized the rDNA of five T. californicus populations from the Pacific Coast of North America and one sample of T. brevicornicus from Scotland. Major findings are as follows: (1) the structural genes for 18S and 28S are highly conserved across T. californicus populations, in contrast to other nuclear and mitochondrial DNA (mtDNA) genes previously studied in these populations. (2) There is extensive differentiation among populations in the IGS region; in the extreme, no homology is observed across the IGS sequences (>2 kb) from the two Tigriopus species. (3) None of the Tigriopus IGS sequences have the subrepeat structure common to other eukaryotic IGS regions. (4) Segregation of rDNA in laboratory crosses indicates that rDNA is located on at least two separate chromosomes in T. californicus. These data suggest that although IGS length polymorphism does not appear to play the adaptive role hypothesized in some other eukaryotic systems, sequence divergence in the rDNA promoter region within the IGS could lead to population specificity of transcription in hybrids.

Copepoda↗

PubMed2005

Intraspecific variation in fem-3 and tra-2, two rapidly coevolving nematode sex-determining genes.

The sex determination gene fem-3 encodes one of the most divergent proteins yet described in the terrestrial nematode Caenorhabditis. Despite this rapid sequence change, however, FEM-3 is essential for male development in the three species surveyed thus far. It also participates in conserved protein-protein complexes with the transmembrane receptor TRA-2 and the phosphatase FEM-2 in these species. These interactions show strong species specificity, indicating that conserved residues are not sufficient for function and that compensatory evolution between binding partners is important. To shed further light on the nature of this coevolution, and to discern the extent of amino acid polymorphism allowed in FEM-3 and the domain of TRA-2 that binds it, we have examined intraspecific variation in the gonochoristic species Caenorhabditis remanei. Ten new complete Cr-fem-3 alleles from three regions of the United States are described. We also obtained sequences for the FEM-3-binding domain of TRA-2 for 9 of the same strains. These alleles were compared with each other, with the European founder alleles, and with the orthologous sequences from the congeners Caenorhabditis elegans and C. briggsae. We find that FEM-3 harbors abundant amino acid polymorphisms along its entire length. The majority (but not all) of these occur in nonconserved residues, and in at least one domain there is evidence for diversifying selection. The FEM-3-binding domain of TRA-2 is less polymorphic than FEM-3. Amino acids neither polymorphic nor conserved between species are candidates for residues mediating species-specific interaction of FEM-3 with its binding partners.

Alleles↗

PubMed2006

Evolutionary origins of the endocannabinoid system.

Endocannabinoid system evolution was estimated by searching for functional orthologs in the genomes of twelve phylogenetically diverse organisms: Homo sapiens, Mus musculus, Takifugu rubripes, Ciona intestinalis, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Arabidopsis thaliana, Plasmodium falciparum, Tetrahymena thermophila, Archaeoglobus fulgidus, and Mycobacterium tuberculosis. Sequences similar to human endocannabinoid exon sequences were derived from filtered BLAST searches, and subjected to phylogenetic testing with ClustalX and tree building programs. Monophyletic clades that agreed with broader phylogenetic evidence (i.e., gene trees displaying topographical congruence with species trees) were considered orthologs. The capacity of orthologs to function as endocannabinoid proteins was predicted with pattern profilers (Pfam, Prosite, TMHMM, and pSORT), and by examining queried sequences for amino acid motifs known to serve critical roles in endocannabinoid protein function (obtained from a database of site-directed mutagenesis studies). This novel transfer of functional information onto gene trees enabled us to better predict the functional origins of the endocannabinoid system. Within this limited number of twelve organisms, the endocannabinoid genes exhibited heterogeneous evolutionary trajectories, with functional orthologs limited to mammals (TRPV1 and GPR55), or vertebrates (CB2 and DAGLbeta), or chordates (MAGL and COX2), or animals (DAGLalpha and CB1-like receptors), or opisthokonta (animals and fungi, NAPE-PLD), or eukaryotes (FAAH). Our methods identified fewer orthologs than did automated annotation systems, such as HomoloGene. Phylogenetic profiles, nonorthologous gene displacement, functional convergence, and coevolution are discussed.

Animals↗

PubMed2005

TAP1 and TAP2 polymorphisms and their linkage disequilibrium with HLA-DR, -DP, and -DQ in an eastern Andalusian population.

Transporter associated with antigen processing (TAP) molecules are involved in the processing of endogenous peptides that bind to major histocompatibility complex (MHC) class I molecules. The possible functional significance of TAP polymorphisms for antigenic peptide transport is an unresolved issue. Population genetics is a tool for investigating the evolutionary and functional significance of genetic polymorphisms. We studied 105 unrelated individuals from Eastern Andalusia in Southern Spain for TAP1 and TAP2 polymorphisms and to detect linkage disequilibrium between TAP1 and TAP2 and between TAP1/TAP2 and human lymphocyte antigen (HLA) DR, DP, and DQ genes. HLA-DR, -DQ, -DP, and TAP1 loci were genotyped with the polymerase chain reaction (PCR)-sequence-specific oligonucleotide method, and TAP2 genes were typed by using the amplification-refractory mutation system-PCR technique. The alleles TAP1*D (3.3%), TAP2*D (2.4%), and TAP2*E (2.9%) were present in the Eastern Andalusian population but not in the general Spanish population. No evidence of linkage disequilibrium was found between TAP1 and TAP2 or between the TAP genes and HLA-DR, -DP, and -DQ in the Eastern Andalusian population. These results are consistent with the absence of coevolution between TAP and MHC class II genes and the hypothesis of selective neutrality.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2005

Local adaptation and enhanced virulence of Nosema granulosis artificially introduced into novel populations of its crustacean host, Gammarus duebeni.

Local adaptation theory predicts that, on average, most parasite species should be locally adapted to their hosts (more suited to hosts from local than distant populations). Local adaptation has been studied for many horizontally transmitted parasites, however, vertically transmitted parasites have received little attention. Here we present the first study of local adaptation in an animal/parasite system where the parasite is vertically transmitted. We investigate local adaptation and patterns of virulence in a crustacean host infected with the vertically transmitted microsporidian Nosema granulosis. Nosema granulosis is vertically transmitted to successive generations of its crustacean host, Gammarus duebeni and infects up to 46% of adult females in natural populations. We investigate local adaptation using artificial horizontal infection of different host populations in the UK. Parasites were artificially inoculated from a donor population into recipient hosts from the sympatric population and into hosts from three allopatric populations in the UK. The parasite was successfully established in hosts from all populations regardless of location, infecting 45% of the recipients. Nosema granulosis was vertically (transovarially) transmitted to 39% of the offspring of artificially infected females. Parasite burden (intensity of infection) in developing embryos differed significantly between host populations and was an order of magnitude higher in the sympatric population, suggesting some degree of host population specificity with the parasite adapted to its local host population. In contrast with natural infections, artificial infection with the parasite resulted in substantial virulence, with reduced host fecundity (24%) and survival (44%) of infected hosts from all the populations regardless of location. We discuss our findings in relation to theories of local adaptation and parasite-host coevolution.

Adaptation, Physiological↗

PubMed2005

Surface carbohydrate composition of a tapeworm in its consecutive intermediate hosts: individual variation and fitness consequences.

Carbohydrates on parasite surfaces have been shown to play an important role in host-parasite coevolution, mediating host non-self recognition and parasite camouflage. Parasites that switch hosts can change their surface molecules to remain undetected by the diverse immune systems of their different hosts. However, the question of individual variation in surface sugar composition and its relation to infectivity, virulence, immune evasion and growth of a parasite in its different hosts is as yet largely unexplored. We studied such fitness consequences of variation in surface sugars in a sympatric host-parasite system consisting of the cestode Schistocephalus solidus and its intermediate hosts, a copepod and the three-spined stickleback. Using lectins to analyse the sugar composition, we show that the tapeworm changes its surface according to the invertebrate or vertebrate host. Importantly, sugar composition seems to be genetically variable, as shown by differences among tapeworm sibships. These differences are related to variation in parasite fitness in its second intermediate host, i.e. infectivity and growth. Surface sugar composition may thus be a proximate correlate of the evolutionarily relevant variability in infectivity and virulence of parasites in different hosts.

Animals↗

PubMed2005

Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers.

Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.

Animals↗

PubMed2006

Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity.

The RNA-catalyzed splicing of group I and group II introns is facilitated by proteins that stabilize the active RNA structure or act as RNA chaperones to disrupt stable inactive structures that are kinetic traps in RNA folding. In Neurospora crassa and Saccharomyces cerevisiae, the latter function is fulfilled by specific DEAD-box proteins, denoted CYT-19 and Mss116p, respectively. Previous studies showed that purified CYT-19 stimulates the in vitro splicing of structurally diverse group I and group II introns, and uses the energy of ATP binding or hydrolysis to resolve kinetic traps. Here, we purified Mss116p and show that it has RNA-dependent ATPase activity, unwinds RNA duplexes in a non-polar fashion, and promotes ATP-independent strand-annealing. Further, we show that Mss116p binds RNA non-specifically and promotes in vitro splicing of both group I and group II intron RNAs, as well as RNA cleavage by the aI5gamma-derived D135 ribozyme. However, Mss116p also has ATP hydrolysis-independent effects on some of these reactions, which are not shared by CYT-19 and may reflect differences in its RNA-binding properties. We also show that a non-mitochondrial DEAD-box protein, yeast Ded1p, can function almost as efficiently as CYT-19 and Mss116p in splicing the yeast aI5gamma group II intron and less efficiently in splicing the bI1 group II intron. Together, our results show that Mss116p, like CYT-19, can act broadly as an RNA chaperone to stimulate the splicing of diverse group I and group II introns, and that Ded1p also has an RNA chaperone activity that can be assayed by its effect on splicing mitochondrial introns. Nevertheless, these DEAD-box protein RNA chaperones are not completely interchangeable and appear to function in somewhat different ways, using biochemical activities that have likely been tuned by coevolution to function optimally on specific RNA substrates.

Adenosine Triphosphate↗

PubMed2005

The evolutionary origin of signa in female Lepidoptera: natural and sexual selection hypotheses.

Signa are structures of the inner wall of the female corpus bursae (structure where males deposit a spermatophore during copulation) of many Lepidoptera that assist in tearing open spermatophores. In this paper, three hypotheses on the evolutionary origin of signa are proposed. The first hypothesis considers natural selection pressures arising from ecological changes that favor an increase in oviposition rate as the force behind the evolution of signa. The other two hypotheses involve sexual selection. The second hypothesis proposes that sexually antagonistic coevolution is responsible of the evolution of signa: According to this hypothesis, the inverse relation between the length of the female's refractory period and the amount of ejaculate remaining in her corpus bursae, observed in most Lepidoptera studied, selects in males a decreased rate of spermatophore digestion (e.g. a thicker spermatophore envelope or a higher chitin content) that increases the length of the refractory period beyond the female's optimum; in response, females evolved signa as a counteradaptation to restore the female's optimum by increasing the rate of spermatophore digestion. The last hypothesis considers that signa may have evolved as a female device for cryptic choice of males based on the ability of these to influence the length of post-copulatory female refractory period. The different hypotheses make different predictions of the sequence of appearance of specific ecological factors and novel phenotypic traits through evolutionary time. Therefore, testing the relative importance of the hypotheses requires a formal comparative analysis.

Adaptation, Physiological↗

PubMed2006

Diversity as a product of inter-specific interactions.

We demonstrate diversification rather than optimization for highly interacting organisms in a well-mixed biological system by means of a simple model of coevolution. We find the cause to be the complex network of interactions formed, allowing species that are less well adapted to an environment to succeed, instead of the 'best' species. This diversification can be considered as the construction of many coevolutionary niches by the network of interactions between species. The model predictions are discussed in relation to experimental work on dense communities of the bacteria Escherichia coli, which may coexist with their own mutants under certain conditions. We find that diversification only occurs above a certain threshold interaction strength, below which competitive exclusion occurs.

Adaptation, Physiological↗

PubMed2006

Autumn colours and the nutrient retranslocation hypothesis: a theoretical assessment.

The adaptive value of the bright colours of leaves in autumn is still debated. It is possible that autumn colours are an adaptation to protect the tree against photoinibition and photooxidation, which allows a more efficient recovery of nutrients. It has been proposed that the preference of aphids for trees that retranslocate nitrogen more efficiently can explain the high diversity of aphids on tree species with bright autumn colours. This scenario however does not take into account the impact of insects on the fitness of the trees and has not been analysed theoretically. Its assumptions and predictions, therefore, remain uncertain. I show with a model of insect-tree interaction that the system can actually evolve under particular conditions. I discuss the differences with the coevolution theory of autumn colours, available evidence and possible tests.

Adaptation, Physiological↗

PubMed2005

Evolution of myelin proteolipid proteins: gene duplication in teleosts and expression pattern divergence.

The coevolution of neurons and their supporting glia to the highly specialized axon-myelin unit included the recruitment of proteolipids as neuronal glycoproteins (DMbeta, DMgamma) or myelin proteins (DMalpha/PLP/DM20). Consistent with a genome duplication at the root of teleosts, we identified three proteolipid pairs in zebrafish, termed DMalpha1 and DMalpha2, DMbeta1 and DMbeta2, DMgamma1 and DMgamma2. The paralogous amino acid sequences diverged remarkably after gene duplication, indicating functional specialization. Each proteolipid has adopted a distinct spatio-temporal expression pattern in neural progenitors, neurons, and in glia. DMalpha2, the closest homolog to mammalian PLP/DM20, is coexpressed with P0 in oligodendrocytes and upregulated after optic nerve lesion. DMgamma2 is expressed in multipotential stem cells, and the other four proteolipids are confined to subsets of CNS neurons. Comparing protein sequences and gene structures from birds, teleosts, one urochordate species, and four invertebrates, we have reconstructed major steps in the evolution of proteolipids.

Amino Acid Sequence↗

PubMed2005

Amino acid sequence constraint and gene expression pattern across the life history in the malaria parasite Plasmodium falciparum.

The relationship between gene expression across the life cycle and protein conservation in Plasmodium falciparum was examined by comparing gene expression data for six life-history stages with the number of nonsynonymous substitutions per site dN between 901 orthologous gene pairs of P. falciparum and Plasmodium yoelii. A high level of expression across the life history was associated with decreased dN and thus with protein conservation. By contrast, differential expression in the sporozoite and merozoite stages was associated with increased dN. At least some sporozoite- and merozoite-expressed genes with high dN have probably been subject to positive selection arising from parasite-host coevolution. A high level of expression across the life history was associated with higher than average G+C content at the first and second codon positions, whereas a high level of expression in the sporozoite and merozoite was associated with reduced G+C content at the first and second codon positions, the latter pattern evidently reflecting the relaxation of constraint on the amino acid sequence.

Amino Acid Sequence↗

PubMed2006

Analysis of Claviceps africana and C. sorghi from India using AFLPs, EF-1alpha gene intron 4, and beta-tubulin gene intron 3.

Isolates of Claviceps causing ergot on sorghum in India were analysed by AFLP analysis, and by analysis of DNA sequences of the EF-1alpha gene intron 4 and beta-tubulin gene intron 3 region. Of 89 isolates assayed from six states in India, four were determined to be C. sorghi, and the rest C. africana. A relatively low level of genetic diversity was observed within the Indian C. africana population. No evidence of genetic exchange between C. africana and C. sorghi was observed in either AFLP or DNA sequence analysis. Phylogenetic analysis was conducted using DNA sequences from 14 different Claviceps species. A multigene phylogeny based on the EF-1alpha gene intron 4, the beta-tubulin gene intron 3 region, and rDNA showed that C. sorghi grouped most closely with C. gigantea and C. africana. Although the Claviceps species we analysed were closely related, they colonize hosts that are taxonomically very distinct suggesting that there is no direct coevolution of Claviceps with its hosts.

Base Sequence↗

PubMed2006

Evolutionary differentiation of Cetartiodactyl placentae in the light of the viviparity-driven conflict hypothesis.

We analysed the evolution of placental traits in the novel mammalian clade Cetartiodactyla (Cetaceans and Artiodactyls) by a parsimony-based computer program (MacClade). A diffuse epitheliochorial placenta was identified as the stem species pattern of this clade. Trophoblast giant cells (TGCs) independently evolved in Camelids and Ruminants. The polycotyledonary placenta is an apomorphic character for Pecora (higher ruminants) and the oligocotyledonary placenta developed as a further step on the stem lineage of cervidae and moschidae. We interpret these findings by application of the "viviparity-driven conflict hypothesis", which states that divergent interests of mother and offspring lead to a rapid antagonistic coevolution, which might cause placental diversity. According to this hypothesis the evolution of camelid and ruminant TGCs can be interpreted as means to increase fetal endocrine influence on the maternal metabolism. The development of the cotyledonary placenta could be related to a diminished availability of glucose, which is associated with the evolution of forestomach fermentation in Pecora. An arms race, in which the mother tried to restrict and the fetus tried to increase transplacental glucose flow, might have promoted the evolution of the cotyledonary placenta, which has a high feto-maternal exchange area, but a low conductivity for glucose.

Adaptation, Physiological↗

PubMed2005

Speciation in parasites: a population genetics approach.

Parasite speciation and host-parasite coevolution should be studied at both macroevolutionary and microevolutionary levels. Studies on a macroevolutionary scale provide an essential framework for understanding the origins of parasite lineages and the patterns of diversification. However, because coevolutionary interactions can be highly divergent across time and space, it is important to quantify and compare the phylogeographic variation in both the host and the parasite throughout their geographical range. Furthermore, to evaluate demographic parameters that are relevant to population genetics structure, such as effective population size and parasite transmission, parasite populations must be studied using neutral genetic markers. Previous emphasis on larger-scale studies means that the connection between microevolutionary and macroevolutionary events is poorly explored. In this article, we focus on the spatial fragmentation of parasites and the population genetics processes behind their diversification in an effort to bridge the micro- and macro-scales.

Animals↗

PubMed2006

Long-term evolution of an ecosystem with spontaneous periodicity of mass extinctions.

Twenty years ago, after analysing palaeontological data, Raup and Sepkoski suggested that mass extinctions on Earth appear cyclically in time with a period of approximately 26 million years (My). To explain the 26My period, a number of proposals were made involving, e.g., astronomical effects, increased volcanic activity, or the Earth's magnetic field reversal, none of which, however, has been confirmed. Here we study a spatially extended discrete model of an ecosystem and show that the periodicity of mass extinctions might be a natural feature of the ecosystem's dynamics and not the result of a periodic external perturbation. In our model, periodic changes of the diversity of an ecosystem and some of its other characteristics are induced by the coevolution of species. In agreement with some palaeontological data, our results show that the longevity of a species depends on the evolutionary stage at which the species is created. Possible further tests of our model are also discussed.

Animals↗