Impacts of a population outbreak of the urchin Tripneustes gratilla amongst Lord Howe Island coral communities

Subtidal reef surveys within the Lord Howe Island Marine Park revealed that populations of the sea urchin Tripneustes gratilla underwent an explosive outbreak in some regions of the park over a 2-year period. This urchin was rare or absent during 2006 surveys at 33 sites studied, but at sites off northern Lord Howe Island in 2008, densities averaged >1.3 m⁻². Dramatic increases in T. gratilla density (exceeding 4 m⁻²) were observed at some sites. We quantify community-level impacts of T. gratilla using ‘before-after’ and ‘control-impact’ data. Zones closed to fishing exhibited similar increases in T. gratilla density to zones open to fishing. Although not previously reported as a keystone species affecting coral habitat, T. gratilla was found to possess an ‘ecosystem engineer’ function. Outbreak sites were characterised by significant declines in cover of foliose algae, including red algae, which decreased from 11.2% in 2006 compared to 2.5% in 2008. Brown foliose algae also declined at sites where T. gratilla outbreaks occurred, averaging 20.4% in 2006 compared to 1.8% in 2008. By contrast, crustose coralline algal cover increased at sites where high T. gratilla densities were observed, from 2.7% in 2006 to an average of 42.6% in 2008. We found no clear indication of impacts on sessile invertebrates or flow-on effects to other levels of the food web, with no significant change in coral cover or densities of mobile invertebrates or fish populations associated with the T. gratilla outbreak.     

Habitat-dependent growth in a Caribbean sea urchin <Emphasis Type="Italic">Tripneustes ventricosus</Emphasis>: the importance of food type

The sea urchin Tripneustes ventricosus is a common, yet relatively poorly known, grazer of seagrass beds and coral reefs throughout the Caribbean. We compared the size and abundance of urchins between adjacent seagrass and coral reef habitats (where macroalgae are the dominant primary producers). We also conducted a laboratory experiment comparing the growth rate of juvenile urchins fed a diet of either macroalgae or seagrass. Reef urchins had significantly larger test diameter than those in the seagrass on some sampling dates. This size difference may be at least partially explained by diet, because laboratory-reared urchins fed macroalgae grew significantly faster than those fed seagrass. The seagrass population, however, was stable over time, whereas the reef population exhibited strong fluctuations in abundance. Overall, our study indicates that both the seagrass and coral reef habitats are capable of supporting healthy, reproductive populations of T. ventricosus. Each, however, appears to offer a distinct advantage: faster growth on the reef and greater population stability in the seagrass.     

Evolution of bindin in the pantropical sea urchin Tripneustes: comparisons to bindin of other genera

Bindin, a sea urchin sperm protein, mediates sperm-egg attachment and membrane fusion and is thus important in species recognition and speciation. Patterns of bindin variation differed among three genera that had been studied previously. In two genera of the superorder Camarodonta, Echinometra and Strongylocentrotus, both of which contain sympatric species, bindin is highly variable within and between species; a region of the molecule evolves at high rates under strong positive selection. In Arbacia, which belongs to the superorder Stirodonta and whose extant species are all allopatric, bindin variation is low, and there is no evidence of positive selection. We cloned and sequenced bindin from Tripneustes, a sea urchin that belongs to the Camarodonta but whose three species are found in different oceans. Worldwide sampling of bindin alleles shows that the bindin of Tripneustes (1) contains the highly conserved core characteristic of all other bindins characterized to date, (2) has an intron in the same position, and (3) has approximately the same length. Its structure is more like that of bindin from other camarodont sea urchins than to bindin from the stirodont ARBACIA: The resemblances to other camarodonts include a glycine-rich repeat structure upstream of the core and lack of a hydrophobic domain 3' of the core, a characteristic of Arbacia bindin. Yet the mode of evolution of Tripneustes bindin is more like that of Arbacia. Differences between bindins of the Caribbean Tripneustes ventricosus and the eastern Pacific T. depressus, separated for 3 my by the Isthmus of Panama, are limited to four amino acid changes and a single indel. There are no fixed amino acid differences or indels between T. depressus from the eastern Pacific and T. gratilla from the Indo-Pacific. Bindin of Tripneustes, like that of Arbacia, also shows no evidence of diversifying selection that would manifest itself in a higher proportion of amino acid replacements than of silent nucleotide substitutions. When the rate of intrageneric bindin divergence is standardized by dividing it by cytochrome oxidase I (COI) divergence, Tripneustes and Arbacia show a lower ratio of bindin to COI substitutions between the species of each genus than exists between the species of either Echinometra or Strongylocentrotus. Thus, mode of bindin evolution is not correlated with phylogenetic affinities or molecular structure, but rather with whether the species in a genus are allopatric or sympatric. For a molecule involved in gametic recognition, this would suggest a pattern of evolution via reinforcement. However, in bindin the process that gave rise to this pattern is not likely to have been selection to avoid hybridization, because there is no excess of amino acid replacements between species versus within species in the bindins of Echinometra and Strongylocentrotus, as would have been expected if specific recognition were the driving force in their evolution. We suggest instead that the pattern of reinforcement is a secondary effect of the ability of species with rapidly evolving bindins to coexist in sympatry.     

Phylogeography of the pantropical sea urchin Tripneustes: contrasting patterns of population structure between oceans

To understand how allopatric speciation proceeds, we need information on barriers to gene flow, their antiquity, and their efficacy. For marine organisms with planktonic larvae, much of this information can only be obtained through the determination of divergence between populations. We evaluated the importance of ocean barriers by studying the mitochondrial DNA phylogeography of Tripneustes, a pantropical genus of shallow water sea urchin. A region of cytochrome oxidase I (COI) was sequenced in 187 individuals from locations around the globe. The COI phylogeny agreed with a previously published phylogeny of bindin that barriers important to the evolution of Tripneustes are: (1) the cold water upwelling close to the tip of South Africa, (2) the Isthmus of Panama, (3) the long stretch of deep water separating the eastern from the western Atlantic, and (4) the freshwater plume of the Orinoco and the Amazon rivers between the Caribbean and the coast of Brazil. These barriers have previously been shown to be important in at least a subset of the shallow water marine organisms in which phylogeography has been studied. In contrast, the Eastern Pacific Barrier, 5000 km of deep water between the central and the eastern Pacific that has caused the deepest splits in other genera of sea urchins, is remarkably unimportant as a cause of genetic subdivision in Tripneustes. There is also no discernible subdivision between the Pacific and Indian Ocean populations of this genus. The most common COI haplotype is found in the eastern, central, and western Pacific as well as the Indian Ocean. Morphology, COI, and bindin data agree that T. depressus from the eastern Pacific and T. gratilla from the western Pacific are, in fact, the same species. The distribution of haplotype differences in the Indo-Pacific exhibits characteristics expected from a sea urchin genus with ephemeral local populations, but with high fecundity, dispersal, and growth: there is little phylogenetic structure, and mismatch distributions conform to models of recent population expansion on a nearly global scale. Yet, comparisons between local populations produce large and significant F(ST) values, indicating nonrandom haplotype distribution. This apparent local differentiation is only weakly reflected in regional divergence, and there is no evidence of isolation by distance in correlations between F(ST) values and either geographical or current distance. Thus, Tripneustes in the Indo-Pacific (but not in the Atlantic) seems to be one large metapopulation spanning two oceans and containing chaotic, nonequilibrium local variation, produced by the haphazard arrival of larvae or by unpredictable local extinction.     

Best Dressed Test: A Study of the Covering Behavior of the Collector Urchin Tripneustes gratilla

Many sea urchin genera exhibit cryptic covering behaviors. One such behavior has been documented in the sea urchin Tripneustes gratilla, and previous studies have theorized that this behavior serves as protection from UV radiation. However, other hypotheses have been presented such as protection from predators or added weight to help T. gratilla resist strong currents. A field study was conducted in October-November 2015 in Moorea, French Polynesia to assess urchin covering behavior in natural habitats. The study found that urchins partially underneath rocks covered more, and with more algae, than urchins totally underneath rocks. To test if this behavior was driven by light intensity, a series of 30-minute experimental trials were run on 10 individuals in bright and dim conditions. Individuals were given red and clear plastic, and percent cover of each was recorded. These tests were repeated once fifty percent of spines had been removed from the urchin, in order to determine whether spine loss affects T. gratilla covering behavior. The study found that urchins had a distinct preference for cover that best protects them from UV radiation. Spine loss did not significantly affect urchin ability to cover, and urchins with removed spines still preferred opaque cover. Additionally, covering behavior was mapped onto a phylogeny of echinoderms to determine how it might have evolved. Understanding urchin covering behavior more fully is a step towards an understanding of the evolution of cryptic behavior across species.     

A multiplex panel of microsatellite markers for widespread sub‐Saharan rodents of the genus Mastomys

We isolated and characterized 12 polymorphic microsatellite loci in the sub‐Saharan rodent Mastomys huberti. We tested cross‐species amplification of all these loci in three closely related Mastomys species: M. coucha, M. erythroleucus and M. natalensis. Multiplex panels comprising 11 loci were developed and their application to a set of individuals in each species allowed clear and easy characterization of allele sizes. Statistics from 31 M. huberti coming from one locality in Mali showed no deviation from Hardy–Weinberg equilibrium except for one locus, and no significant linkage disequilibria between loci.     

The cotton-top tamarin revisited: Mhc class I polymorphism of wild tamarins,and polymorphism and allelic diversity of the class II DQA1, DQB1, and DRB loci

Cotton-top tamarins (Saguinus oedipus) in captivity are unusual in that they exhibit low levels of polymorphism and allelic diversity at the major histocompatibility complex (Mhc) class I loci. Since the polymorphism has previously only been examined in captive tamarins, we analyzed the Mhc class I alleles of a population of wild tamarins. These wild tamarins, like their captive counterparts, exhibited limited class I polymorphism. We also assessed the levels of polymorphism and allelic diversity at the Mhc class II DQA1, DQB1, DQB2, and the DRB loci in captive populations of cotton-top tamarins. In contrast to the extensive polymorphism in Old World monkeys, only two alleles were detected at each of DQA1 and DQB1. Also, the DQB2 locus was monomorphic and conserved between New and Old World monkeys. Sequences derived from four putative DRB loci were obtained, and extensive polymorphism was found at all four loci. Phylogenetic analysis did not indicate that any of the tamarin DRB loci, with the possible exception of Saoe-DRB3, were orthologous to the human DRB loci. At three of the DRB loci (Saoe-DRB11, Saoe-DRB ^* W12, Saoe-DRB ^* W22), the number of nonsynonymous changes was higher than the number of synonymous changes in the putative antigen recognition sites, indicative of positive selection. We found no support for a restriction on the polymorphism at the cotton-top tamarin class II loci. However, the allelic diversity at some of the Saoe-DRB loci is more limited than for the HLA-DRB1, consistent with a restriction imposed by the bone marrow-chimerical lifestyle.     

Eleven polymorphic microsatellite loci for the salmonid trematode Plagioporus shawi

We isolated and characterized 11 microsatellite loci from Plagioporus shawi, a parasitic trematode of salmonid fishes (Oncorhynchus spp.). Extensive polymorphism (expected heterozygosities ranging from 0.476 to 0.981 and number of alleles from 10 to 55) was found in a sample of 94 trematodes from 24 infected cutthroat trout (Oncorhynchus clarki) individuals. Nine of the 11 loci will be useful for future genetic studies on within population dynamics of P. shawi.     

Isolation of polymorphic microsatellite loci in the ponerine ant Ectatomma tuberculatum

We report the development of 11 microsatellite markers by an enrichment protocol in the ponerine ant Ectatomma tuberculatum. Polymorphism was explored in two colonies collected from Mexico and two colonies from Brazil. From the 11 loci which amplified, seven loci showed intracolonial polymorphism in Mexican colonies and only six loci were variable in populations from Brazil. Observed heterozygosity ranged from 0.18 to 0.84. The other five loci exhibited different alleles between Mexico and Brazil but geographical variability was not investigated further. Cross‐amplification was tested in another species of the same Tribe (Gnamptogenys striatula) and one locus was revealed to be polymorphic.     

Isolation and characterization of microsatellite loci from the rust pathogen,Melampsora lini

We developed and characterized primers for 11 variable microsatellite loci present in the genome of the flax rust, Melampsora lini. The microsatellite loci were identified by sequencing clones from a library of EcoRI DNA fragments enriched for four simple sequence repeat motifs (AAG, AAT, TC and TG). All 11 primer pairs successfully amplified DNA fragments from a sample of 102 M. lini isolates (98 isolated from Linum marginale and four from Linum usitatissimum), revealing a total of 32 alleles. Allelic diversity at the 11 loci ranged from 0.030 to 0.449.     

High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae)

The objectives of the present study were to develop microsatellite markers for the wild strawberry, Fragaria virginiana, to evaluate segregation patterns of microsatellite alleles in this octoploid species, and assess genetic variability at microsatellite loci in a wild population. A genomic library was screened for microsatellite repeats and several PCR primers were designed and tested. We also tested the use of heterologous primers and found that F. virginiana primers amplified products in cultivated strawberry, Fragaria × ananassa Duch. and Fragaria chiloensis. Similarly, microsatellite loci developed from cultivated strawberry also successfully amplified F. virginiana loci. We investigated four microsatellite loci in detail, three developed from F. virginiana and one from cultivated strawberry. A survey of 100 individuals from a population of F. virginiana in Pennsylvania demonstrated high heterozygosities (H_e or gene diversity ranged from 0.80 to 0.88 per locus) and allelic diversity (12–17 alleles per locus), but individual plants had no more than two alleles per locus. Segregation patterns in parents and progeny of two controlled crosses at these four loci were consistent with disomic Mendelian inheritance. Together these findings suggest that the genome of F. virginiana is "highly diploidized" and at least a subset of microsatellite loci can be treated as codominant, diploid markers. Significant heterozygote deficiencies were found at three of the four loci for hermaphroditic individuals but for only one locus among females in this gynodioecious species.Communicated by J. Dvorak     

Microsatellite loci for fathead minnow (Pimephales promelas)

We describe the cloning and characterization of seven microsatellite loci (six dinucleotide and one tetranucleotide) from fathead minnow (Pimephales promelas). In a sample of 48 fish from a captive population, polymorphism at these loci ranged from 4 to 11 alleles with expected heterozygosities ranging from 0.59 to 0.82. These loci will be extremely useful to researchers currently studying the ecotoxicology, behaviour and population genetics of this species.     

Isolation and characterization of microsatellites in Aphidius ervi (Hymenoptera: Braconidae) and their applicability to related species

Aphidius ervi (Hymenoptera: Braconidae) is an important biological control agent of aphids, and a model organism for the study of host–parasitoid ecology and evolution. We isolated microsatellite loci from A. ervi to examine the genetic effects of its introduction from Europe to North America. We present primers for 11 microsatellites from A. ervi. We have assayed six of these loci for variability and found from two to 37 alleles. These six primer pairs were tested on 17 related species and appear broadly applicable. These microsatellite loci provide a new tool for research on A. ervi and its relatives.     

Associations between quantitative traits and enzyme loci in the F2 population of a maize hybrid

Summary Univariate and multivariate analyses were used to identify associations between eight enzyme marker loci and 11 quantitative traits of maize (Zea mays L.). The material analyzed included inbred lines Wf9 and Pa405, single-cross hybrid Wf9 X Pa405, and the F2 generation of the selfed single-cross hybrid. Each enzyme locus assayed was associated with at least one quantitative trait, and all quantitative traits were associated with genotypes at particular enzyme loci. Significant associations also were found between the level of heterozygosity per individual and nine of 11 quantitative traits. The total contribution to heterosis, for seed yield per plant, of genes linked with the eight enzyme loci, was 27% of the F2 mean and 18% of the difference in mean between the F1 hybrid and the inbred parents. Genes linked with Glu1 accounted for nearly one third of the total dominance effect detected by the eight enzyme loci. The chromosome segments marked by loci with significant effects on seed yield were markedly overdominant. The large heterotic effects of chromosome segments marked by particular loci suggest that enzyme loci could be used to help transfer genes responsible for heterosis to inbred lines. We conclude that analyses of additional inbred lines, F1 hybrids, and F2 populations in more environments will halp identify specific associations between enzyme loci, or chromosome segments which they mark, and important agronomic traits.Cooperative investigations of the USDA, ARS and Dept. of Plant Sciences, South Dakota State Univ. (SDSU), Brookings, Journal Series No. 2039; and the Institute of Animal Resource Ecology, Univ. of British Columbia, Vancouver, B.C. V6T 1W5, Canada     

Development and optimization of microsatellite DNA primers for boreal owls (Aegolius funereus)

We developed 22 microsatellite loci for boreal owls (Aegolius funereus). We genotyped 275 unrelated boreal owls (Aegolius f. richardsoni) and 36 unrelated Tengmalm's owls (Aegolius f. funereus) using seven loci that were polymorphic and did not have detectable null alleles. Among North American and Scandinavian boreal owls, respectively, allelic diversity ranged from three to 11 alleles and from one to 11 alleles, observed heterozygosity ranged from 0.31 to 0.80 and from 0.00 to 0.81, and expected heterozygosity ranged from 0.28 to 0.81 and from 0.00 to 0.81. These markers appeared to amplify DNA in six other Strigidae species.     

Characterization of microsatellite loci isolated from the blacktip shark and their utility in requiem and hammerhead sharks

We isolated and characterized 16 microsatellite loci from the blacktip shark, Carcharhinus limbatus, and tested cross‐species amplification in 11 Carcharhinus species and five additional shark genera. Thirty‐six (1.6%) and 180 (48%) colonies were positive for dinucleotide repeat motifs from unenriched and enriched libraries, respectively. Heterozygosities of polymorphic loci ranged from 0.04 to 0.96 with two to 22 alleles per locus. Amplification products were observed at nine to 13 loci (five to 11 of which where polymorphic) in 10 Carcharhinus species. Several loci were also polymorphic in each of the additional genera examined.     

Testing for the Effects of Seasonal and Lunar Periodicity on the Reproduction of the Edible Sea Urchin <Emphasis Type="Italic">Tripneustes gratilla</Emphasis> (L) in Kenyan Coral Reef Lagoons

The annual and lunar reproductive cycle of the widely distributed edible sea urchin Tripneustes gratilla (L) was examined through measurements of gonad index, histological examination of gametogenesis, and induction of spawning with KCl injections. The population density and morphological characteristics of urchins at Diani, Kanamai, and Vipingo reef lagoons were also studied as well as the effects of seawater temperature and light on reproduction. Gonad growth started early during the northeast monsoon and reached a peak in June at the beginning of the southeast monsoon followed by a sharp decrease in gonad size of 50% in July and August towards the end of the southeast monsoons. Histological examination of gonads, revealed many different stages of gametogenesis with gametes present throughout the year, indicating continuous reproduction. There was a significant relationship between gonad index and lunar day with spawning occurring between lunar day 7 and 21, but spawning was not in perfect synchrony in the population. The population density of urchins at each reef is variable from year to year and was highest on average at Vipingo. Urchins at Kanamai had the lowest gonad indices, the largest jaws and smallest individuals an indication of food limitation. The gonads (roe) of T. gratilla at all three sites, were perpetually ‘runny’ an attribute that is not suitable for urchin fisheries. Studies to develop techniques to improve roe quality are recommended.     

Isolation and characterisation of polymorphic microsatellite markers for the endangered ferreous limpet <Emphasis Type="Italic">Patella ferruginea</Emphasis> (Gastropoda,Patellidae)

The limpet Patella ferruginea is one of the most endangered marine invertebrates on western Mediterranean rocky shores. We have isolated and characterised 11 polymorphic microsatellites markers to provide new tools to investigate genetic structure and gather information necessary for the proper management of this severely threatened species. The number of alleles per locus ranged from 2 to 16 (mean; Na = 8.37) with an average observed heterozygosity of 0.64 (He = 0.66). The levels of polymorphism uncovered at these loci suggest that they should be useful for population genetic studies, parentage analysis and assessment of connectivity among protected areas. None of the pairwaise comparisons among loci showed significant linkage disequilibrium after sequential Bonferroni correction. All but one locus (Pf-31IF1) conformed to HW equilibrium. Further investigation revealed that departures at Pf-31IF1 were not caused by null alleles. Results from cross-species amplifications suggest that some of these loci may also be useful for Patella tenuis (two loci) P. ulyssiponensis (one locus) and P. piperata (three loci).     

A revised leopard frog phylogeny allows a more detailed examination of adaptive evolution at ranatuerin-2 antimicrobial peptide loci

Ranatuerins are antimicrobial peptides of the innate immune system found in ranid frogs. We previously presented evidence that a positive selective sweep had fixed a single allele at the Ranatuerin2 locus in the northern leopard frog (Rana pipiens). In this paper, we further investigate the evolutionary history of ranatuerins as follows. First, we sequenced Ranatuerin2 in additional individuals of R. pipiens and related frog species and compared diversity and divergence at these sequences with that at four putatively neutrally evolving loci. Second, we asked whether the evolutionary patterns observed at Ranatuerin2 were typical for ranatuerin loci by sequencing our samples at a paralogous locus, Ranatuerin2b, and performing the same neutrality tests. Ranatuerin2b also showed strong and significant evidence of at least one selective sweep. Third, we used the neutral loci to independently resolve conflicting hypotheses about phylogenetic relationships among our study species. Both the neutral loci and the ranatuerin loci supported an older phylogeny inferred from allozyme data and strongly rejected a more recent phylogeny inferred from mitochondrial DNA. Finally, in order to test whether the sweep was driven by the evolution of substantially new peptide function, we used the phylogeny to reconstruct the hypothetical Ranatuerin2 peptide that existed before the sweep. We synthesized this peptide and tested its activity and that of the extant peptide against six bacterial pathogens of frogs. We observed antibacterial activity but found no significant functional differences between the two peptides.     

Is local adaptation in Mimulus guttatus caused by trade‐offs at individual loci?

Local adaptation is considered to be the result of fitness trade‐offs for particular phenotypes across different habitats. However, it is unclear whether such phenotypic trade‐offs exist at the level of individual genetic loci. Local adaptation could arise from trade‐offs of alternative alleles at individual loci or by complementary sets of loci with different fitness effects of alleles in one habitat but selective neutrality in the alternative habitat. To evaluate the genome‐wide basis of local adaptation, we performed a field‐based quantitative trait locus (QTL) mapping experiment on recombinant inbred lines (RILs) created from coastal perennial and inland annual races of the yellow monkeyflower (Mimulus guttatus) grown reciprocally in native parental habitats. Overall, we detected 19 QTLs affecting one or more of 16 traits measured in two environments, most of small effect. We identified 15 additional QTL effects at two previously identified candidate QTLs [DIV ERGENCE (DIV)]. Significant QTL by environment interactions were detected at the DIV loci, which was largely attributable to genotypic differences at a single field site. We found no detectable evidence for trade‐offs for any one component of fitness, although DIV2 showed a trade‐off involving different fitness traits between sites, suggesting that local adaptation is largely controlled by non‐overlapping loci. This is surprising for an outcrosser, implying that reduced gene flow prevents the evolution of individuals adapted to multiple environments. We also determined that native genotypes were not uniformly adaptive, possibly reflecting fixed mutational load in one of the populations.