Characterization of microsatellite loci isolated in midget faded rattlesnake (Crotalus viridis concolor)

Primers for five polymorphic microsatellite loci were developed for the midget faded rattlesnake (Crotalus viridis concolor), a rare subspecies of western rattlesnake (Crotalus viridus) found only in parts of Wyoming, Colorado, and Utah. Five polymorphic microsatellites were isolated, four of which had relatively high levels of diversity (eight to nine alleles). We found only two departures from Hardy–Weinberg equilibrium and they occurred in different loci, so null alleles are likely not a problem. Moreover, we found that no two loci were linked. These loci will be applicable for population genetic analysis and perhaps analysis of paternity and mating systems.     

Habitat selection and the colonization of new territories by Chromis viridis

The settlement and recruitment patterns of Chromis viridis were followed during three consecutive seasons along the reefs of Eilat, Red Sea. The findings, based on intensive field surveys and a translocation experiment, indicated a strong and repeatable preference for some, but not other, colonies of the branching coral Acropora eurystoma; with significantly more larvae settling onto preferred colonies that house conspecific adults and juveniles. Furthermore, these findings showed that, given high recruitment rates, settlement‐site selection could drive migration by adults and older juveniles. As only some C. viridis schools received direct settlement, it was suggested that settlement‐driven migration is responsible for the replenishment of those schools that do not receive settlement and to the colonization of previously unoccupied coral colonies.     

Comparative genome scan detects host‐related divergent selection in the grasshopper Hesperotettix viridis

In this study, we used a comparative genome scan to examine patterns of population differentiation with respect to host plant use in Hesperotettix viridis, a Nearctic oligophagous grasshopper locally specialized on various Asteraceae including Solidago, Gutierrezia, and Ericameria. We identified amplified fragment length polymorphism (AFLP) loci with significantly elevated F_ST (outlier loci) in multiple different‐host and same‐host comparisons of populations while controlling for geographic distance. By comparing the number and identities of outlier loci in different‐host vs. same‐host comparisons, we found evidence of host plant‐related divergent selection for some population comparisons (Solidago‐ vs. Gutierrezia‐feeders), while other comparisons (Ericameria‐ vs. Gutierrezia‐feeders) failed to demonstrate a strong role for host association in population differentiation. In comparisons of Solidago‐ vs. Gutierrezia‐feeding populations, a relatively high number of outlier loci observed repeatedly in different‐host comparisons (35% of all outliers and 2.7% of all 625 AFLP loci) indicated a significant role for host‐related selection in contributing to overall genomic differentiation in this grasshopper. Mitochondrial DNA sequence data revealed a star‐shaped phylogeny with no host‐ or geography‐related structure, low nucleotide diversity, and high haplotype diversity, suggesting a recent population expansion. mtDNA data do not suggest a long period of isolation in separate glacial refugia but are instead more compatible with a single glacial refugium and more recent divergence in host use. Our study adds to research documenting heterogeneity in differentiation across the genome as a consequence of divergent natural selection, a phenomenon that may occur as part of the process of ecological speciation.     

Species-specific ability ofChlorella strains (Chlorophyceae) to form stable symbioses withHydra viridis

46 strains ofChlorella, identified by physiological and biochemical characters, were examined for their ability to form stable symbioses with aposymbioticHydra viridis. It was found to be a species-specific characteristic. Among the 15 taxa studied, onlyC. saccharophila var.ellipsoidea, C. saccharophila var.saccharophila, C. fusca var.vacuolata, C. kessleri, C. luteoviridis, andC. protothecoides formed stable symbioses withHydra viridis. Among the 11 known physiological and biochemical characters of theseChlorella species, only acid tolerance seems to be correlated with symbiosis: All symbiotic species are capable of growing at or below pH 4.0.     

Development and characterization of microsatellite markers for the walking goby (Scartelaos viridis; Gobiidae)

Scartelaos viridis (walking goby) is a small edible fish that inhabits warm inshore environments. To provide molecular information of S. viridis, we developed and characterized microsatellite markers for this species. Using (CA)15-enriched genomic libraries of Scartelaos viridis, 44 positive clones were sequenced; 34 sequences contained multiple repeat motifs (di-, tri- and tetra-nucleotide). In all, 23 primer pairs were designed and 15 were successfully amplified. Forty-two S. viridis individuals collected from the East China Sea were used to characterize the polymorphism at each locus. Three loci (13%) were polymorphic, with three to six alleles. The observed and expected heterozygosity ranged from 0.1000 to 0.4500 and from 0.4487 to 0.7580, respectively. The polymorphism information content per locus ranged from 0.4214 to 0.7510. Three loci significantly deviated from the Hardy-Weinberg equilibrium (adjusted P value=0.017); the pairwise tests for linkage disequilibrium between Scvi-1-13 and Scvi-2-11 were significant (P<0.05, adjusted P value=0.017). The low number of polymorphic microsatellite loci may be due to the close genetic relationship of the individuals that we collected and the large size of the motifs.     

Genetic variability in a temperate intertidal Phoronid,Phoronopsis viridis

The Phoronida are a coelomate phylum consisting of only two genera and about 12–15 described species. Phoronids probably represent the common ancestral stock of all lophophorates, and may be the most primitive living deuterostomes. Using the techniques of starch gel electrophoresis, we have studied genetic variation at 39 loci in 120 individuals of Phoronopsis viridis collected in Bodega Harbor, Bodega Bay, California. Allelic variation was found at 27 (69.2%) loci. If a locus is considered polymorphic when the frequency of the most common allele is no greater than 0.99, the proportion of polymorphic loci in the total sample is 48.7%. The average number of alleles per locus is 2.23. The expected frequency of heterozygous loci per individual on the assumption of Hardy-Weinberg equilibrium is 9.4%. There is evidence of inbreeding; the mean value of F, Wright's fixation index, is 0.21±0.02. Genetic variability in P. viridis is intermediate among marine invertebrates. The tropical clam, Tridacna maxima, has on the average 20.2% heterozygous loci per individual. At the other extreme, a brachiopod from Antarctica, Liothyrella notorcadensis, has an average of 3.9% heterozygous loci per individual. Among marine invertebrates, there seems to be a gradient of decreasing genetic variability from low to high latitudes, which may reflect their different adaptive strategies.     

Phylogeography of the Eurasian green woodpecker (Picus viridis)

Aim In this paper we investigate the evolutionary history of the Eurasian green woodpecker (Picus viridis) using molecular markers. We specifically focus on the respective roles of Pleistocene climatic oscillations and geographical barriers in shaping the current population genetics within this species. In addition, we discuss the validity of current species and subspecies limits. Location Western Palaearctic: Europe to western Russia, and Africa north of the Sahara. Methods We sequenced two mitochondrial genes and five nuclear introns for 17 Eurasian green woodpeckers. Multilocus phylogenetic analyses were conducted using maximum likelihood and Bayesian algorithms. In addition, we sequenced a fragment of the cytochrome b gene (cyt b, 427 bp) and of the Z‐linked BRM intron 15 for 113 and 85 individuals, respectively. The latter data set was analysed using population genetic methods. Results Our phylogenetic results support the monophyly of Picus viridis and suggest that this taxon comprises three allopatric/parapatric lineages distributed in North Africa, the Iberian Peninsula and Europe, respectively. The North African lineage split from the Iberian/European clade during the early Pleistocene (1.6–2.2 Ma). The divergence event between the Iberian and the European lineages occurred during the mid‐Pleistocene (0.7–1.2 Ma). Our results also support a post‐glacial range expansion of these two lineages from distinct refugia located in the Iberian Peninsula and possibly in eastern Europe or Anatolia, which led to the establishment of a secondary contact zone in southern France. Main conclusions Our results emphasize the crucial role of both Pleistocene climatic oscillations and geographical barriers (Strait of Gibraltar, Pyrenees chain) in shaping the current genetic structure of the Eurasian green woodpecker. Our molecular data, in combination with diagnosable plumage characters, suggest that the North African green woodpecker (Levaillant’s woodpecker) merits species rank as Picus vaillantii (Malherbe, 1847). The two European lineages could be distinguished by molecular and phenotypic characters over most of their respective geographical ranges, but they locally exchange genes in southern France. Consequently, we prefer to treat them as subspecies (P. viridis viridis, P. viridis sharpei) pending further studies.     

Ultrastructural aspects of kranz anatomy inDigitaria sanguinalis andSetaria viridis (poaceae)

Structural differentiation of Kranz anatomy has been investigated in leaf cross sections of two C-4 Poaceae:Digitaria sanguinalis andSetaria viridis. The study mainly focused on cellular and interfacial features of bundle sheath (BS) and mesophyll (MS) cells of the C-4 structure. Prominent BS, spaced by only two MS cells apart, were surrounded concentrically by a layer of MS cells. BS cells ofS. viridis had centrifugally arranged relatively large chloroplasts containing much starch, but the chloroplasts had agrana to rudimentary grana. Structural and size dimorphisms, when starch was present, were detected between BS and MS chloroplasts. Loosely arranged MS cells had peripherally displaced smaller chloroplasts containing little to none starch. BS chloroplasts ofD. sanguinalis were similar to those ofS. viridis, but had very little starch and well-developed long agranal stroma lamella. Features of MS cells were similar in both species, but well-defined peripheral reticulum (PR) was easily recognized in MS chloroplasts ofS. viridis. Virtually no PR was developed in BS chloroplasts examined. BS cells contained more mitochondria and microbodies, but no structural dimorphism was noticed. The electron-dense suberized lamella were often observed between BS and MS cells, especially in the primary wall of BS cells. It was most frequently found at the BS and MS cell interfaces and terminated in radial walls of the adjacent BS cells. Prominent pits with plasmodesmata (pd) were seen in the walls of both cells. There also were numerous pd in outer tangential walls of the BS cells. The number of pd ranged from 20 to 60. The pd trasversed a segment of cell wall much thinner than the adjacent wall. The current cellular data have been compared to the ultrastructural features known in leaves of other C-4 plants, especially NADP-ME species.     

Isolation and characterization of microsatellite loci in <Emphasis Type="Italic">Melicope quadrilocularis</Emphasis> (Rutaceae), an endemic plant species of the Bonin Islands,Japan, and cross-species amplification in closely related taxa

Twelve microsatellite loci were isolated and characterized for Melicope quadrilocularis, an insular endemic tree species of the Bonin Islands. The observed number of alleles at each locus ranged from 1 to 18. The range of expected heterozygosity was 0.0000–0.9445. The inter-specific applicability of these loci was evaluated by analyzing two other endemic species and one endemic variety of Melicope that are also distributed on the Bonin Islands. All primer pairs for the 12 loci tested successfully amplified the loci in all taxa, except for primers for four loci in M. nishimurae.     

Twelve polymorphic microsatellites in Oriental river prawn, Macrobrachium nipponense

Oriental river prawn, Macrobrachium nipponense, is a commercially important freshwater prawn species in China, Japan, Korea and Vietnam. Due to overfishing for food, the wild stocks M. nipponense are endangered. Twenty microsatellite loci were isolated from the M. nipponense. Twelve of these loci were polymorphic (seven to 16 alleles per locus), with expected heterozygosity ranging from 0.68 to 0.86 (n = 48). These polymorphic loci provide a valuable tool for assessing genetic diversity of wild and cultured populations.     

Inheritance of some Mendelian factors in intra- and interspecific crosses between Setaria italica and Setaria viridis

Summary The inheritance of seed coat color, pericarp color, polyphenoloxidase activity and bristle, glume, collar, and leaf-base anthocyanic colorations was investigated using intra- and interspecific crosses between Setaria italica and S. viridis. The results were compared to inheritance results obtained by previous authors. In most cases, the inheritance is simple (one or two loci) and data from different crosses (intra- and interspecific) and from different authors can be compared. Two sets of two characters were found to share common loci: the polyphenoloxidase locus is one of the loci responsible for seed coat color, and bristle and glume color are determined by the same two loci. The evolutionary significance of these results is discussed.     

Biological Control of the Grasshopper Hesperotettix viridis pratensis by the Nematode Mermis nigrescens

Decline and disappearance of a natural population of the grasshopper Hesperotettix viridis pratensis was related to severe infection by Mermis nigrescens. In contrast the numbers of slightly infected Melanoplus bivittatus did not decrease. Uninfected M. sanguinipes, M. differentialis and M. fernur-rubrum also did not decrease. The high percentage of infection in H. viridis pratensis was related to low, wet habitat, where the grasshopper fed primarily on Solidago missouriensis; infected individuals failed to develop ovaries or mature testes. This is believed to be the first reported occurrence of a nematode parasitizing H. viridis pratensis. In juvenile M. nigrescens the unreported shape of the stoma, the stylet shape and paired oval structures in the cerebral region were photographed. Factors affecting biological control of grasshoppers by using M. nigrescens were discussed.     

Molecular Cloning of a cDNA Encoding Ribosome Inactivating Protein from Amaranthus viridis and Its Expression in E. coli

In order to isolate a cDNA clone of ribosome inactivating protein (RIP), a cDNA library was constructed in Uni-ZAP XL vector with poly(A) RNA purified from leaves of Amaranthus viridis. To get the probe for screening the library, PCR of phage DNA was conducted using the vector primer and degenerate primer designed from a conserved putative active site of the RIPs. Twenty-six cDNA clones from about 600,000 plaques were isolated, and one of these clones was fully sequenced. It was 1,047 bp and contained an open reading frame encoding 270 amino acids. The deduced amino acid sequence had a putative signal sequence of 17 amino acids and a putative active site (AIQMVAEAARFFKYIE) conserved in other RIPs. E. coli cells expressing A. viridis RIP cDNA did not grow well as compared to control cells, indicating that recombinant A. viridis RIP presumably inactivated E. coli ribosomes. In addition, recombinant A. viridis RIP cDNA produced by E. coli had translation inhibition activity in vitro.     

Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of seven-band grouper (Epinephelus septemfasciatus) and cross-species amplification

Seven-band grouper (Epinephelus septemfasciatus) is a commercially important fishery species. Sixty-six microsatellite loci were isolated from a dinucleotide-enriched genomic library of E. septemfasciatus. Twelve of these loci were polymorphic in a test population with alleles per locus ranging from two to five, and observed and expected heterozygosities per locus from 0.04 to 1.00 and from 0.28 to 0.76, respectively. Three loci significantly deviated from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was found between pairs of loci after Bonferroni correction. Cross-species amplification of these polymorphic microsatellite loci was performed in additional two related species. These polymorphic microsatellite loci would be useful for investigating genetic resource of E. septemfasciatus and other related species. Lili Zhao and Changwei Shao have contributed equally.     

PCR primers for polymorphic microsatellite loci in the plant‐ant Azteca ulei cordiae (Formicidae: Dolichoderinae)

Twelve microsatellite loci were isolated from the Peruvian tropical plant‐ant, Azteca ulei cordiae (Hymenoptera: Dolichoderinae). High levels of within‐population variation were observed at most loci, with number of alleles ranging from four to 18, and heterozygosity from 0.118 to 1 per population sample. Cross‐species amplification of these loci was also successfully tested in several other species of the same ant genus Azteca.     

PERMANENT GENETIC RESOURCES: A set of 12 microsatellite loci for genetic studies of Leishmania braziliensis

Twelve microsatellite loci of Leishmania braziliensis were examined, nine of which were developed in this work. Fifty‐six Leishmania braziliensis were genotyped with these microsatellite loci. The 12 loci studied were polymorphic with the number of alleles ranging from five to 19, with a mean of 9.7 ± 4.1 and the observed heterozygosity averaging 0.425 ± 0.202. The important heterozygote deficits we observed (F_IS = 0.41, P value = 0.004) appear incompatible with the heterozygote excess expected in clonal diploids. This last result could revive the clonality/sexuality debate regarding Leishmania. This work validates the potential use of these microsatellites for population genetics analysis.     

The macrophyte, Stratiotes aloides, protects larvae of dragonfly Aeshna viridis against fish predation

Predation could be one force determining which contemporary species occupy a certain habitat. Aeshna viridis is an endangered dragonfly species with a larval distribution strongly associated with lakes where the water plant, water soldier, Stratiotes aloides, occurs. In this study, the larvae were almost exclusively found in patches of S. aloides. To study larval association with S. aloides further, we conducted a series of laboratory experiments. Behavioural experiments indicated that larvae preferred S. aloides. Aeshna viridis larvae were nocturnal and rather inactive. Larvae on S. aloides were less susceptible to predation by the perch, Perca fluviatilis, than larvae on another water plant, Myriophyllum alterniflorum. According to our study it seems that occurrence of S. aloides may limit the distribution of A. viridis, and the protection of refuges may be essential in planning the conservation of this endangered species.     

Microsatellite loci for the southern pine beetle (Dendroctonus frontalis) and cross‐species amplification in Dendroctonus

We developed microsatellite loci for the southern pine beetle (Dendroctonus frontalis). Twelve microsatellite loci were identified. Eight loci were polymorphic and sufficiently variable in 62 individuals (expected heterozygosity ranged from 0.707 to 0.880) to investigate population structure. All loci conformed to HWE except Dfr‐14, which showed heterozygote excess, and no two loci deviated from linkage equilibrium. The loci were tested for cross‐species amplification in four species of Dendroctonus (D. valens, D. terebrans, D. brevicomis, and D. ponderosae). Seven loci were polymorphic in at least one of the species tested.     

Microsatellite loci for Dawson's burrowing bee (Amegilla dawsoni) and their cross‐utility in other Amegilla species

Microsatellite loci were isolated from Dawson's burrowing bee, Amegilla dawsoni, a species endemic to Western Australia. Twelve polymorphic loci were found with an observed number of alleles ranging from two to 24 and observed heterozygosities between 0.17 and 0.85. These 12 loci were tested for amplification in three additional species of Amegilla. The loci will be used for sex determination and the examination of mating frequency in this species.     

Isolation and characterization of microsatellite loci from chub Leuciscus cephalus (Pisces: Cyprinidae)

Twelve microsatellite markers were isolated from chub Leuciscus cephalus Linné, 1766 (Cyprinidae), a freshwater fish widely distributed in Europe. We assessed the level of genetic diversity for these loci in 24 individuals sampled in the Rhone river watershed. Nine loci were polymorphic, displaying from two to 13 alleles per locus with expected heterozygosity ranging from 0.160 to 0.887. Simultaneous migration of different polymerase chain reaction products was developed for routine analysis of L. cephalus populations.