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Sex, bugs and Haldane's rule: the nematode genus Pristionchus in the United States.

BACKGROUND: The nematode Pristionchus pacificus has been developed as a satellite organism in evolutionary developmental biology for comparison to Caenorhabditis elegans. Comparative studies have revealed major differences in the regulation of developmental processes between P. pacificus and C. elegans. To place evolutionary developmental biology and the observed developmental differences between species in a comprehensive evolutionary context, such studies have to be complemented with ecological aspects. Knowledge about the ecology of the organism in question might indicate specific environmental conditions that can result in developmental adaptations and could account for species differences in development. To this end, we have started to investigate the ecology of Pristionchus nematodes. In recent field studies in Western Europe we found six Pristionchus species that are closely associated with scarab beetles and the Colorado potato beetle. This Pristionchus-beetle association provides the unique opportunity to combine research in evolutionary developmental biology with ecology. However, it remains unknown how general these findings from Europe are on a global scale. RESULTS: Here, we describe the Pristionchus species associated with scarab and Colorado potato beetles in the Eastern United States and show striking transatlantic differences and unexpected evolutionary and ecological patterns. Two hundred eighty of 285 (98%) isolates from American scarab beetles belong to five Pristionchus species, all of which are different from the European species. We describe four of them as novel Pristionchus species. The five American Pristionchus species fall into a single phylogenetic clade and have a male-female (gonochoristic) mode of reproduction, whereas the majority of European isolates are hermaphroditic. Crosses between the two most closely related species, P. aerivorus and P. pseudaerivorus n. sp., follow Haldane's rule in that heterogametic F1 males are inviable. We observed P. aerivorus and P. pseudaerivorus n. sp. coexisting on the same scarab beetle and obtained two cases of F1 hybrids from wild beetles. Finally, the Colorado potato beetle is associated with the same nematode, P. uniformis in the United States and Europe. Given the introduction of the Colorado potato beetle to Europe in 1877, our results suggest that P. uniformis was introduced together with its beetle vector. CONCLUSION: Taken together, the Pristionchus-beetle association provides a powerful tool for studying biodiversity, biogeography, speciation and species invasion on a global scale.

Journal Article↗

Assessment of the diversity and species specificity of the mutualistic association between Epicephala moths and Glochidion trees.

The obligate mutualisms between flowering plants and their seed-parasitic pollinators constitute fascinating examples of interspecific mutualisms, which are often characterized by high levels of species diversity and reciprocal species specificity. The diversification in these mutualisms has been thought to occur through simultaneous speciation of the partners, mediated by tight reciprocal adaptation; however, recent studies cast doubt over this general view. In this study, we examine the diversity and species specificity of Epicephala moths (Gracillariidae) that pollinate Glochidion trees (Phyllanthaceae), using analysis of mitochondrial and nuclear gene sequences. Phylogenetic analysis of Epicephala moths associated with five Glochidion species in Japan and Taiwan reveal six genetically isolated species that are also distinguishable by male genital morphology: (i) two species specific to single host species (G. acuminatum and G. zeylanicum, respectively); (ii) two species that coexist on G. lanceolatum; and (iii) two species that share two, closely-related parapatric hosts (G. obovatum and G. rubrum). Statistical analysis shows that the two species associated with G. lanceolatum are not sister species, indicating the colonization of novel Glochidion host in at least one lineage. Behavioural observations suggest that all six species possess the actively-pollinating habit, thus none of the studied species has become a nonmutualistic 'cheater' that exploits the benefit resulting from pollination by other species. Our results parallel recent findings in ecologically similar associations, namely the fig-fig wasp and yucca-yucca moth mutualisms, and contribute to a more general understanding of the factors that determine ecological and evolutionary outcomes in these mutualisms.

Adaptation, Physiological↗

Unique growth and morphology properties of Clade 5 Clostridioides difficile strains revealed by single-cell time-lapse microscopy.

Clostridioides difficile is a gastrointestinal pathogen of both humans and agricultural animals and thus a major One Health threat. The C. difficile species consists of five main clades, with Clade 5 currently undergoing speciation from Clades 1-4. Clade 5 strains are highly prevalent in agricultural animals and can cause zoonotic infections, suggesting that these strains have evolved phenotypes that distinguish them from Clade 1-4 strains. Here, we compare the growth properties of Clade 5 strains to those of Clade 1-4 strains using anaerobic time-lapse microscopy coupled with automated image analysis. Our analyses indicate that Clade 5 strains grow faster and are more likely to form long chains of cells than Clade 1-4 strains. Using comparative genomic and CRISPRi analyses, we show that the chaining phenotype of Clade 5 strains is driven by the orientation of the invertible cmr switch sequence, with chaining strains exhibiting a bias to the cmr-ON state. Interestingly, Clade 5 strains with a bias towards the cmr-ON state shifted to a largely cmr-OFF state during murine infection, suggesting that the cmr-OFF state is under positive selection during infection. Collectively, our data reveal that Clade 5 strains have distinct growth properties, which may allow them to inhabit diverse ecological niches.

Journal Article↗

On the elusiveness of enemy-free space: spatial, temporal, and host-plant-related variation in parasitoid attack rates on three gallmakers of goldenrods.

Host shifting by phytophagous insects may play an important role in generating insect diversity by initiating host-race formation and speciation. Models of the host shifting process often invoke reduced rates of natural enemy attack on a novel host in order to balance the maladaptation expected following the shift. Such "enemy-free space" has been documented for some insects, at some times and places, but few studies have assessed the occurrence of enemy-free space across years, among sites, or among insect species. We measured parasitoid attack rates on three insect herbivores of two goldenrods (Solidago altissima L. and Solidago gigantea Ait.), with data from multiple sites and multiple years for each herbivore. For each insect herbivore, there were times and sites at which parasitoid attack rates differed strongly and significantly between host plants (that is, enemy-free space existed on one host plant or the other). However, the extent and even the direction of the attack-rate difference varied strongly among sites and even among years at the same site. There was no evidence of consistent enemy-free space for any herbivore on either host plant. Our data suggest that enemy-free space, like many ecological and evolutionary forces, is likely to operate as a geographic and temporal mosaic, and that conceptual models of host shifting that include enemy-free space as a consequence of host novelty are likely too simple.

Animals↗

Unique growth and morphology properties of Clade 5 Clostridioides difficile strains revealed by single-cell time-lapse microscopy.

Clostridioides difficile is a gastrointestinal pathogen of both humans and agricultural animals and thus a major One Health threat. The C. difficile species consists of five main clades, with Clade 5 currently undergoing speciation from Clades 1-4. Since Clade 5 strains are highly prevalent in agricultural animals and a frequent cause of zoonotic infections, these strains may have evolved phenotypes that distinguish them from Clade 1-4 strains. Here, we compare the growth properties of Clade 5 strains to those of Clade 1-4 strains using anaerobic time-lapse microscopy coupled with automated image analysis. Our analyses indicate that Clade 5 strains grow faster and are more likely to form long chains of cells than Clade 1-4 strains. Using comparative genomic and CRISPRi analyses, we show that the chaining phenotype of Clade 5 strains is driven by the orientation of the invertible cmr switch sequence, with chaining strains exhibiting a bias to the cmr-ON state. Interestingly, Clade 5 strains with a bias towards the cmr-ON state shifted to a largely cmr-OFF state during murine infection, suggesting that the cmr-OFF state is under positive selection during infection. Collectively, our data reveal that Clade 5 strains have distinct growth properties, which may allow them to inhabit diverse ecological niches.

Clostridioides difficile↗

Columbines: a geographically widespread species flock.

Species in the columbine genus, Aquilegia, are known for their broad variation in ecology and floral morphology. Aquilegia is also known for the large degree of intercompatibility among its species, which has led to the suggestion that the genus has arisen recently. However, intercompatibility does not always imply recent divergence and the widespread distribution pattern of the genus has suggested an older age. We constructed phylogenies for Aquilegia plus its close relatives by using nucleotide sequence data from both nuclear and chloroplast DNA. The sequence data averaged over 1250 bp per species. Among the 14 columbine species sampled from Europe, Asia, and North America only 16-bp changes and one insertion/deletion event were detected. In contrast, related genera had from 3 to 45 times this level of variation. The phylogenies derived from the chloroplast and nuclear DNA sequences were highly concordant and suggest that the columbines are the result of a recent, rapid radiation. In contrast to other examples of species flocks, Aquilegia has radiated on a widespread geographical scale. By comparison with their related taxa, we suggest that the evolution of the nectar spur in Aquilegia was a key innovation for this genus and allowed rapid speciation through specialization to specific pollinators.

Base Sequence↗

Adaptive radiation in microbial microcosms.

It has often been argued that evolutionary diversification is the result of divergent natural selection for specialization on alternative resources. I provide a comprehensive review of experiments that examine the ecology and genetics of resource specialization and adaptive radiation in microbial microcosms. In these experiments, resource heterogeneity generates divergent selection for specialization on alternative resources. At a molecular level, the evolution of specialization is generally attributable to mutations that de-regulate the expression of existing biosynthetic and catabolic pathways. Trade-offs are associated with the evolution of resource specialization, but these trade-offs are often not the result of antagonistic pleiotropy. Replicate adaptive radiations result in the evolution of a similar assemblage of specialists, but the genetic basis of specialization differs in replicate radiations. The implications of microbial selection experiments for evolutionary theory are discussed and future directions of research are proposed.

Adaptation, Biological↗

Isolation and characterization of a MHC class II DRB locus in the European water vole (Arvicola terrestris).

In so-called model species, such as human and mouse, genes of the major histocompatibility complex (MHC) are characterized by extremely high levels of polymorphism, and it is considered that such diversity is maintained by balancing selection. ;There is now a recognized need to expand studies into nonmodel species to examine whether high MHC diversity is mirrored in natural populations, and to determine the ecological, ethological, and evolutionary processes that underpin balancing selection. To address such issues, a necessary prerequisite is the ability to characterize diversity at a single, expressed, polymorphic MHC locus on which selection may be acting. Here, we provide the first description of allelic diversity at exon 2 of an MHC class II DRB locus in the European water vole (Arvicola terrestris), characterize variation across four natural populations, and test whether the patterns of variation are consistent with the effects of balancing selection. Using single-strand conformation polymorphism analysis and subsequent DNA sequencing of gel excisions, five DRB alleles were resolved, each with a unique amino acid sequence, among 100 individuals from four geographically distinct populations. Reverse transcription polymerase chain reaction confirmed that the alleles were products from an expressed locus. Intra-allelic amino acid differences were high (10.5-33.3%), and the nonsynonymous substitution rate exceeded the synonymous substitution rate for the functional peptide-binding region (d (N):d (S)=3.91 and P<0.005). Phylogenetic comparison of resolved alleles with closely related homologues indicated that each allele represented a unique lineage preserved across speciation events. These results indicate that balancing selection has maintained diversity of DRB allelic lineages and amino acid function over evolutionary time scales, but may be less effective at preserving alleles in contemporary populations where stochastic microevolutionary processes may dominate.

Alleles↗

Parasite species coexistence and limiting similarity: a multiscale look at phylogenetic, functional and reproductive distances.

The factors that control biodiversity have been the focus of numerous recent investigations; these include species interactions, speciation, environmental gradients and heterogeneity, all of these operating differently at each observation scale. We used a null model to examine the influence of two forces shaping the community structure of Dactylogyrus species parasitic on roach (Rutilus rutilus) gills: interspecific competition that might prevent the coexistence of the most similar species and environmental filters that might result in the most similar species coexisting together. The study was carried out on two sets of fish from two different localities in the Morava river basin (Czech Republic) to evaluate the consistency of the results across host populations, and at three different scales of observation to test for the scale dependence of assembly rules. In decreasing order, from largest to smallest, the three spatial scales investigated were: the individual fish, the individual gill arch and individual sections of each gill arch. The similarity between pairs of parasite species was measured using three different criteria: (1) phylogeny, (2) quantitative functional traits consisting of parasite size and morphometric measurements of the attachment organ's sclerotized parts and (3) qualitative attributes of reproductive organs. First, our study reveals a strong conservatism of ecological characters for the nine Dactylogyrus parasite species, in particular regarding the attributes of their copulatory organs. Second, our study did not find any limitation of similarity among coexisting Dactylogyrus species due to interspecific competition, irrespective of the scale and the similarity measures considered. Conversely, our results support the niche filtering hypothesis, preventing the co-occurrence of species too dissimilar from one another. This process is particularly apparent at the scale of the individual fish and for functional traits associated with the hard parts of the parasites' attachment organs. In both localities, the Dactylogyrus species that occur on the same fish individuals tend to have similar values for the haptor dimensions. Our study supports previous studies on monogenean parasite communities indicating a weak influence of competition as a structuring force, but it goes a step further by identifying environmental filtering as a key process shaping these communities.

Animals↗

Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression.

We applied genome-wide gene expression analysis to the evolutionary processes of adaptive speciation of the Israeli blind subterranean mole rats of the Spalax ehrenbergi superspecies. The four Israeli allospecies climatically and adaptively radiated into the cooler, mesic northern domain (N) and warmer, xeric southern domain (S). The kidney and brain mRNAs of two N and two S animals were examined through cross-species hybridizations with two types of Affymetrix arrays (mouse and rat) and muscle mRNA of six N and six S animals with spotted cDNA mouse arrays. The initial microarray analysis was hypothesis-free, i.e., conducted without reference to the origin of animals. Principal component analysis revealed that 20-30% of the expression signal variability could be explained by the differentiation of N-S species. Similar N-S effects were obtained for all tissues and types of arrays: two Affymetrix microarrays using probe oligomer signals and the spotted array. Likewise, ANOVA and t test statistics demonstrated significant N-S ecogeographic divergence and region-tissue specificity in gene expression. Analysis of differential gene expression between species corroborates previous results deduced by allozymes and DNA molecular polymorphisms. Functional categories show significant N-S ecologic putative adaptive divergent up-regulation of genes highlighting a higher metabolism in N, and potential adaptive brain activity and kidney urine cycle pathways in S. The present results confirm ecologic-genomic separation of blind mole rats into N and S. Gene expression regulation appears to be central to the evolution of blind mole rats.

Adaptation, Physiological↗

Polyphyly and gene flow between non-sibling Heliconius species.

BACKGROUND: The view that gene flow between related animal species is rare and evolutionarily unimportant largely antedates sensitive molecular techniques. Here we use DNA sequencing to investigate a pair of morphologically and ecologically divergent, non-sibling butterfly species, Heliconius cydno and H. melpomene (Lepidoptera: Nymphalidae), whose distributions overlap in Central and Northwestern South America. RESULTS: In these taxa, we sequenced 30-45 haplotypes per locus of a mitochondrial region containing the genes for cytochrome oxidase subunits I and II (CoI/CoII), and intron-spanning fragments of three unlinked nuclear loci: triose-phosphate isomerase (Tpi), mannose-6-phosphate isomerase (Mpi) and cubitus interruptus (Ci) genes. A fifth gene, dopa decarboxylase (Ddc) produced sequence data likely to be from different duplicate loci in some of the taxa, and so was excluded. Mitochondrial and Tpi genealogies are consistent with reciprocal monophyly, whereas sympatric populations of the species in Panama share identical or similar Mpi and Ci haplotypes, giving rise to genealogical polyphyly at the species level despite evidence for rapid sequence divergence at these genes between geographic races of H. melpomene. CONCLUSION: Recent transfer of Mpi haplotypes between species is strongly supported, but there is no evidence for introgression at the other three loci. Our results demonstrate that the boundaries between animal species can remain selectively porous to gene flow long after speciation, and that introgression, even between non-sibling species, can be an important factor in animal evolution. Interspecific gene flow is demonstrated here for the first time in Heliconius and may provide a route for the transfer of switch-gene adaptations for Müllerian mimicry. The results also forcefully demonstrate how reliance on a single locus may give an erroneous picture of the overall genealogical history of speciation and gene flow.

Animals↗

Correlates of species richness in mammals: body size, life history, and ecology.

We present the most extensive examination to date of proposed correlates of species richness. We use rigorous phylogenetic comparative techniques, data for 1,692 mammal species in four clades, and multivariate statistics to test four hypotheses about species richness and compare the evidence for each. Overall, we find strong support for the life-history model of diversification. Species richness is significantly correlated with shorter gestation period in the carnivores and large litter size in marsupials. These traits and short interbirth intervals are also associated with species richness in a pooled analysis of all four clades. Additionally, we find some support for the abundance hypotheses in different clades of mammals: abundance correlates positively with species richness in primates but negatively in microchiropterans. Our analyses provide no evidence that mammalian species richness is associated with body size or degree of sexual dimorphism.

Animals↗

Molecular signatures of adaptive introgression and selection in contact zones of closely related pine species (Pinus genus).

BACKGROUND: Natural hybridization plays a key role in shaping genetic diversity, local adaptation, and the dynamics of speciation through interspecific gene flow. Hybrid zones serve as valuable natural systems for studying these processes. In this research, we used genotypic data at thousands of nuclear SNPs to investigate genomic outcomes of hybridization and selection across three contact zones of closely related pine species including Scots pine (Pinus sylvestris L.) and dwarf mountain pine (P. mugo T.). Reference allopatric stands of parental species were used to assess introgression dynamics. RESULTS: Individuals from the hybrid zones showed distinct genetic ancestry patterns and were assigned to groups including putative pure species, first-generation hybrids, and advanced backcrosses. Genotypes of the majority of hybrids were shifted towards P. mugo ancestry. Most outlier loci were shared across all sympatric populations, although some were specific to individual contact zones. The identified outliers were mainly associated with regulatory biological processes related to phosphorylation, proteolysis, and transmembrane transport. Signatures of local adaptation varied in different genetic classes in contact zones and they were strongest in pure P. sylvestris and hybrids with a majority of P. sylvestris ancestry. The pattern suggests that it may be driven by adaptation to peat bog habitats situated outside the species&#x2019; core ecological niche. CONCLUSIONS: Our findings indicate strong selective pressure acting on multiple genes in groups of hybrids and pure Pinus sylvestris individuals across all studied hybrid zones. In contrast, the weaker signal of selection observed in individuals with P. mugo ancestry suggests that relict populations of this species, which historically spread across postglacial peat bogs, were pre-adapted to such environments. While several outlier loci were shared across different contact zones, others were unique for one of them, indicating that local environmental pressures and adaptive introgression shape the genomic composition of the populations. These results highlight the role of hybridization in generating adaptive diversity and emphasize the evolutionary significance of hybrid zones in pines.

Hybridization, Genetic↗

Life cycles shape parasite evolution: comparative population genetics of salmon trematodes.

Little is known about what controls effective sizes and migration rates among parasite populations. Such data are important given the medical, veterinary, and economic (e.g., fisheries) impacts of many parasites. The autogenic-allogenic hypothesis, which describes ecological patterns of parasite distribution, provided the foundation on which we studied the effects of life cycles on the distribution of genetic variation within and among parasite populations. The hypothesis states that parasites cycling only in freshwater hosts (autogenic life cycle) will be more limited in their dispersal ability among aquatic habitats than parasites cycling through freshwater and terrestrial hosts (allogenic life cycle). By extending this hypothesis to the level of intraspecific genetic variation, we examined the effects of host dispersal on parasite gene flow. Our a priori prediction was that for a given geographic range, autogenic parasites would have lower gene flow among subpopulations. We compared intraspecific mitochondrial DNA variation for three described species of trematodes that infect salmonid fishes. As predicted, autogenic species had much more highly structured populations and much lower gene flow among subpopulations than an allogenic species sampled from the same locations. In addition, a cryptic species was identified for one of the autogenic trematodes. These results show how variation in life cycles can shape parasite evolution by predisposing them to vastly different genetic structures. Thus, we propose that knowledge of parasite life cycles will help predict important evolutionary processes such as speciation, coevolution, and the spread of drug resistance.

Analysis of Variance↗

Levels of genetic polymorphism: marker loci versus quantitative traits.

Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species.

Alleles↗

Size, morphology and composition of particulates in aquatic ecosystems: solving speciation problems by correlative electron microscopy.

Particulates can impact directly on aquatic ecosystems by determining the availability and mode of dispersion of both contaminants and nutrients. An understanding of the mechanisms of such particle-associated phenomena is being augmented by particle analysis technology. In this context, microscopic and spectroscopic techniques, devised for problem solving, are being applied to frequently encountered sub-micrometre particulates which are 'unstable' with respect to methods of sample preparation and storage used routinely for particulates prior to analysis. These unstable aquatic particulates include 'species' sensitive to dehydration and to artificial aggregation induced by surfaces within a fractionation apparatus. These species, as defined broadly, include polysaccharide gels, hydrated humic substances, iron oxyhydroxides, viruses, the smallest micro-organisms and decomposing parts of cells. To develop predictive models of their roles as dispersing agents for contaminants, and to speciate such associations, it is necessary to characterize them in a state as close to the natural as possible. This critical review presents the state-of-the-art in the realistic characterization of hydrated sub-micrometre particulates by correlative electron microscopy (EM) used in conjunction with spectroscopy and minimally perturbing preparatory techniques. Correlative EM is a strategy for using several different kinds of microscopes and accessory techniques in a multi-method context to analyse a given specimen for different kinds of information, including relationships in three dimensions within colloid systems. Sizing, morphology and gross composition are determined on a 'per particle' basis by transmission EM used in conjunction with energy-dispersive spectroscopy, electron diffraction and molecule-specific stains.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Aluminum in acidic surface waters: chemistry, transport, and effects.

Ecologically significant concentrations of Al have been reported in surface waters draining "acid-sensitive" watersheds that are receiving elevated inputs of acidic deposition. It has been hypothesized that mineral acids from atmospheric deposition have remobilized Al previously precipitated within the soil during soil development. This Al is then thought to be transported to adjacent surface waters. Dissolved mononuclear Al occurs as aquo Al, as well as OH-, F-, SO4(2-), and organic complexes. Although past investigations have often ignored non-hydroxide complexes of Al, it appears that organic and F complexes are the predominant forms of Al in dilute (low ionic strength) acidic surface waters. The concentration of inorganic forms of Al increases exponentially with decreases in solution pH. This response is similar to the theoretical pH dependent solubility of Al mineral phases. The concentration of organic forms of Al, however, is strongly correlated with variations in organic carbon concentration of surface waters rather than pH. Elevated concentrations of Al in dilute acidic waters are of interest because: Al is an important pH buffer; Al may influence the cycling of important elements like P, organic carbon, and trace metals; and Al is potentially toxic to aquatic organisms. An understanding of the aqueous speciation of Al is essential for an evaluation of these processes.

Acids↗

Numerical simulation of iodine speciation in relation to water disinfection aboard manned spacecraft I. Equilibria.

Elemental iodine (I2) is currently used as the drinking water disinfectant aboard the Shuttle Orbiter and will also be incorporated into the water recovery and distribution system for the International Space Station Alpha. Controlled release of I2 is achieved using the Microbial Check Valve (MCV), a flow-through device containing an iodinated polymer which imparts a bacteriostatic residual concentration of approximately 2mg/L to the aqueous stream. During regeneration of MCV canisters, I2 concentrations of approximately 300 mg/L are used. Dissolved iodine undergoes a series of hydrolytic disproportionation and related reactions which result in the formation of an array of inorganic species including: I-, I3-, HOI, OI-, IO3-, HIO3, I2OH-, I2O(-2), and H2OI+. Numerical estimation of the steady-state distribution of inorganic iodine containing species in pure water at 25 degrees C has been achieved by simultaneous solution of the multiple equilibrium expressions as a function of pH. The results are reported herein.

Disinfection↗