Genome-wide polymorphisms show unexpected targets of natural selection

Natural selection can act on all the expressed genes of an individual, leaving signatures of genetic differentiation or diversity at many loci across the genome. New power to assay these genome-wide effects of selection comes from associating multi-locus patterns of polymorphism with gene expression and function. Here, we performed one of the first genome-wide surveys in a marine species, comparing purple sea urchins, Strongylocentrotus purpuratus, from two distant locations along the species' wide latitudinal range. We examined 9112 polymorphic loci from upstream non-coding and coding regions of genes for signatures of selection with respect to gene function and tissue- and ontogenetic gene expression. We found that genetic differentiation (F(ST)) varied significantly across functional gene classes. The strongest enrichment occurred in the upstream regions of E3 ligase genes, enzymes known to regulate protein abundance during development and environmental stress. We found enrichment for high heterozygosity in genes directly involved in immune response, particularly NALP genes, which mediate pro-inflammatory signals during bacterial infection. We also found higher heterozygosity in immune genes in the southern population, where disease incidence and pathogen diversity are greater. Similar to the major histocompatibility complex in mammals, balancing selection may enhance genetic diversity in the innate immune system genes of this invertebrate. Overall, our results show that how genome-wide polymorphism data coupled with growing databases on gene function and expression can combine to detect otherwise hidden signals of selection in natural populations.     

Positive Darwinian selection in gamete recognition proteins of Strongylocentrotus sea urchins

Gamete recognition proteins commonly experience positive Darwinian selection and evolve more rapidly than nonreproductive proteins, but the selective forces responsible for their adaptive diversification remain unclear. We examined the patterns of positive selection in the cognate interacting pair of proteins formed by sperm bindin and its egg receptor (EBR1) and in two regions of the sea urchin sperm receptor for egg jelly suREJ3 gene (exons 22 and 26) among four species of Strongylocentrotus sea urchins (S. purpuratus, S. droebachiensis, S. pallidus and S. franciscanus). The signatures of selection differed at each reproductive protein. A strong signal of positive selection was detected at bindin in all lineages even though the species compared had highly variable gamete traits and experience different intensities and forms of sexual selection and sexual conflict in nature. Weaker selection was observed at EBR1 but the small region studied precluded a clear understanding of the extent of sexual conflict between bindin and the EBR1 protein. At the suREJ3 locus, diversifying selection was observed in exon 22 but not exon 26, suggesting that these regions experience different selective pressures and evolutionary constraints. Positive selection was also detected within S. pallidus at suREJ‐22 because of the presence of 12 amino acid replacement mutations segregating at frequencies >0.10. Our results suggest that sexual conflict may be the predominant evolutionary mechanism driving the rapid diversification of reproductive proteins between, and polymorphism within, strongylocentrotid sea urchins.     

Gastrulation in the Sea Urchin,Strongylocentrotus purpuratus,Is Disrupted by the Small Laminin Peptides YIGSR and IKVAV

Laminin is present on the apical and basolateral sides of epithelial cells of very early sea urchin blastulae. We investigated whether small laminin-peptides, known to have cell binding activities, alter the development of sea urchin embryos. The peptide YIGSR-NH₂ (850 μM) and the peptide PA22-2 (5 μM), which contains the peptide sequence IKVAV (Tashiro et al., J. Biol. Chem. 264, 16174, 1989), typically blocked archenteron formation when added to the sea water soon after fertilization. At lower doses, the YIGSR peptide allowed invagination of the archenteron but blocked archenteron extension and differentiation and evagination of the feeding arms. The effect of YIGSR and PA22-2 peptides declined when added to progressively older stages until no effect was seen when added at the mesenchyme blastula stage (24 hours after fertilization). Control peptides GRGDS, YIGSE, and SHA22, a dodeca-peptide with a scrambled IKVAV sequence, had no effect on development. The YIGSK peptide containing a conserved amino acid modification had only a small effect on gastrulation. The results suggest that YIGSR and IKVAV peptides specifically disrupt cell/extracellular matrix interactions required for normal development of the archenteron and feeding arms. Our recent finding that YTGIR is at the cell binding site of the B1 chain of S. purpuratus laminin supports this conclusion. Evidently, laminin or other laminin-like molecules are among the many extracellular matrix components needed for the invagination and extension of the archenteron during the gastrulation movements of these embryos.     

Annual reversible plasticity of feeding structures: cyclical changes of jaw allometry in a sea urchin

A wide variety of organisms show morphologically plastic responses to environmental stressors but in general these changes are not reversible. Though less common, reversible morphological structures are shown by a range of species in response to changes in predators, competitors or food. Theoretical analysis indicates that reversible plasticity increases fitness if organisms are long-lived relative to the frequency of changes in the stressor and morphological changes are rapid. Many sea urchin species show differences in the sizes of jaws (demi-pyramids) of the feeding apparatus, Aristotle''s lantern, relative to overall body size, and these differences have been correlated with available food. The question addressed here is whether reversible changes of relative jaw size occur in the field as available food changes with season. Monthly samples of the North American Pacific coast sea urchin Strongylocentrotus purpuratus were collected from Gregory Point on the Oregon (USA) coast and showed an annual cycle of relative jaw size together with a linear trend from 2007 to 2009. Strongylocentrotus purpuratus is a long-lived species and under field conditions individuals experience multiple episodes of changes in food resources both seasonally and from year to year. Their rapid and reversible jaw plasticity fits well with theoretical expectations.     

Tektin interactions and a model for molecular functions

Tektins from echinoderm flagella were analyzed for microheterogeneity, self-associations and association with tubulin, resulting in a general model of tektin filament structure and function applicable to most eukaryotic cilia and flagella. Using a new antibody to tektin consensus peptide RPNVELCRD, well-characterized chain-specific antibodies and quantitative gel densitometry, tektins A, B and C were found to be present in equimolar amounts in Sarkosyl-urea-stable filaments. In addition, two isoforms of tektin A are present in half-molar ratios to tektins B and C. Cross-linking of AB filaments indicates in situ nearest neighbor associations of tektin A1B and A2B heterodimers, -trimers, -tetramers and higher oligomers. Soluble purified tektin C is cross-linked as homodimers, trimers and tetramers, but not higher oligomers. Tektin filaments associate with both loosely bound and tightly bound tubulin, and with the latter in a 1:1 molar ratio, implying a specific, periodic association of tightly bound tubulin along the tektin axis. Similarly, in tektin-containing Sarkosyl-stable protofilament ribbons, two polypeptides ( approximately 67/73 kDa, homologues of rib72, efhc1 and efhc2) are present in equimolar ratios to each other and to individual tektins, co-fractionating with loosely bound tubulin. These results suggest a super-coiled arrangement of tektin filaments, the organization of which has important implications for the evolution, assembly and functions of cilia and flagella.     

Organismal defenses versus environmentally mediated protection from herbivores: Unraveling the puzzling case of Desmarestia viridis (Phaeophyta)

The role of anti-herbivore organismal defenses in algae-herbivore interaction is frequently investigated without taking into account the potential role of environmental factors in mediating the interaction. Here we reexamine the interaction between the highly acidic, brown alga Desmarestia viridis and the green sea urchin, Strongylocentrotus droebachiensis, by incorporating a previously overlooked facet, the effect of changes in the wave environment on the ability of the urchin to establish contact with the alga. Factorial experiments in a wave tank (presence versus absence of waves; real versus mimic algae) showed that the aggregation of urchins on D. viridis was more than 2-fold greater in the absence than in the presence of waves. Similar numbers of urchins made contact with natural and mimic D. viridis plants, both with and without waves, indicating that any external release of chemicals (acid) from the alga had no perceptible repulsive effect on the urchin. The ability of the urchins to climb onto D. viridis increased markedly when urchin density attained a critical level. These results were consistent with field observations that urchins readily attack D. viridis under conditions of low wave action but do not under conditions of moderate wave action. We conclude (1) that the chemical makeup of D. viridis alone is neither necessary nor sufficient to limit contacts by the urchins and that (2) wave action is a major factor explaining the survival of D. viridis on urchin barrens, because waves limit the movements of the urchins towards the alga. We recommend that studies addressing marine algal defenses against herbivores be more comprehensive and examine interactions between algal traits, the physical environment, and the abundance and behavioral repertoire of herbivores.     

Changes in growth and reproduction of green sea urchins, Strongylocentrotus droebachiensis (Müller), during repopulation of the shallow subtidal zone after mass mortality

Following a disease outbreak that caused mass mortality of green sea urchins, Strongylocentrotus droebachiensis, along the Atlantic coast of Nova Scotia in September 1999, changes in growth and reproduction were monitored over 3.75 years as surviving individuals migrated from deep water to repopulate the shallow subtidal zone at a wave-exposed site. Urchins were sampled at 4 depth strata: at 24 m on a boulder field where the population was unaffected by the disease, at 12 and 16 m on a steeply sloping bedrock ramp, and at 8-10 m along the lower margin of a kelp bed (Laminaria digitata) where urchins formed a grazing front by January 2002. Urchins migrating shoreward from the deep-water refuge responded rapidly to increased algal productivity in the shallows through increased growth and reproduction. Measures of annual increments of skeletal elements (rotules) from urchins across the depth gradient indicated that the fastest growing individuals from the source population formed the grazing front. Urchins in the front reached a larger asymptotic size and produced larger gonads than urchins lower on the ramp. The annual cycle in gonad index showed a pronounced spring spawning period across all depths; a secondary fall spawning was evident at the front and 12 m. The presence of mature, fertilizable ova and short response time to spawning induction in both spring and fall supported the occurrence of two spawning periods.     

Biochemical and pathogenic properties of the natural isolate of Shewanella algae from Peter the Great Bay, Sea of Japan

Pathogenic properties of the natural isolate of Shewanella algae from the coelomic fluid of the sea cucumber Apostichopus japonicus (Peter the Great Bay, Sea of Japan) were investigated. The isolate had oxydative metabolism, was positive for ornithine decarboxylase, cytochrome oxidase, catalase, DNase and gelatinase, hemolytically active, did not produce acid from carbohydrates, and did not hydrolyze urea and esculin. The strain was resistant to penicillin, amoxicillin, and ampicillin and susceptible to tetracycline and carbenicillin. Among cellular fatty acids, 13:0-i, 15:0-i, 16:0, 16:1(n-7), 17:0-i, and 17:0-ai dominated. These biochemical properties made it possible to attribute the isolated bacteria to the genus Shewanella and identified as S. algae. The cells of this bacterium were introduced into the coelomic cavity of another echinoderm, the sea urchin Strongylocentrotus nudus. As a result, in about 24 h the animals became slow and 3-8 days after the inoculation died. Dividing bacteria were being found during the experiment in the coelomic fluid as well as in the phagosomes of amoebocytes, i.e. cells acting as phagocytes in the coelomic fluid. The studies of the invasive properties of strain 156 showed that bacterial cells entered the subcuticular space of S. nudus and A. japonicus through the cuticle and stayed there for a long time without penetrating epithelium and exerting toxic effect upon the organisms of the laboratory animals. Pathogenic effect of S. algae can be manifested only if the cutaneous epithelium is destroyed permitting it to penetrate the lower tissue layers. The toxicity of S. algae is confirmed by in vitro experiments. The inoculation of the embryonic cells of S. nudus with samples of this bacterium caused the death of 10% of cells within an hour and 100% of cells within 12 h after inoculation. The results of the investigations demonstrate that S. algae could produce opportunistic infection in the sea cucumber A. japonicus and the sea urchin S. nudus, which may be natural reservoirs of this human pathogen.