Isolation and characterization of novel microsatellite loci for the short‐beaked common dolphin (Delphinus delphis) and cross‐amplification in other cetacean species

Seven tetranucleotide and three dinucleotide microsatellite loci were isolated from the short‐beaked common dolphin (Delphinus delphis). Number of alleles and observed heterozygosity ranged from three to twelve (mean 8.4) and from 0.087 to 0.978 (mean 0.741), respectively. All loci were tested in four other odontocete species and showed polymorphisms in most locus–species combinations. This panel of nuclear markers will be useful for the investigation of population ecology and social interactions in common dolphins and other cetacean species.     

Development of microsatellite markers for parentage analysis in the great tinamou (Tinamus major)

Eighteen microsatellite loci were isolated from great tinamous (Tinamus major), which are large terrestrial birds found in the Neotropics. These are the first primers developed for the Order Tinamiformes. Paternity analyses are possible because the levels of heterozygosity are sufficiently high (0.29-0.90).     

Microsatellite markers for the tambaqui (Colossoma macropomum, Serrasalmidae, Characiformes), an economically important keystone species of the Amazon River floodplain

Colossoma macropomum is a keystone species of the Amazon floodplain, and is an important but severely overexploited commercial species. To provide tools for addressing ecological and conservation questions, we developed 14 highly polymorphic microsatellite markers that had between four and 21 alleles per locus in the 25 tested individuals. With the exception of comparisons involving the locus Cm1F5 that also showed heterozygosity deficiency, no pairs of loci were at linkage disequilibrium. Many of the microsatellite loci were also variable in three other serrasalmid species which span the phylogenetic depth of the Serrasalmidae.     

Particulate organic carbon, sterols, fatty acids and pigments in the Amazon River system

Water samples were collected from the Amazon River system during a high flood period, in June 1989, and lipids associated with particles retained on GF/F filters were examined. Particles showed a highly variable organic carbon content (1.8–29.0%). Corresponding organic carbon concentrations varied from 0.36 to 1.13 mg/l. The flood conditions encountered during the sampling period may feed exceptional inputs of soil organic matter into the tributaries and the Amazon River. Composition and concentration of sterols, fatty acids and pigments were determined to estimate the relative portion of terrigenous and autochthonous fraction of this complex organic matter. Sterol distribution patterns were similar to other equatorial rivers, in the Orinoco (Venezuela) and Solo (Indonesia). In comparison with the dominant profile of the Amazon system, distinct patterns were found in the Trombetas River (29^5,22 27⁵ 29⁵ 28⁵, 28^5,22) and in the Tapajos River (27^5,22 > 27⁵ 29⁵, 28⁵, 28^5,22). These fingerprints reflect different vegetation types of drainage basins and distinct planktonic pools. The distribution of even-carbon numbered saturated fatty acids in the carbon range of 24–36 revealed low inputs of constituents associated with cuticular waxes of vascular plants in Black waters and in the Tapajos River (200 ng/l), higher in White waters (328–483 ng/l) and highest in the Trombetas River (704 ng/l) and in stagnant waters of a small lake close to the Amazon (1088 ng/l). Pigment concentrations showed that in the main river and most tributaries vegetal carbon did not represent more than 2%, except for the Tapajos River (6.2%) and in relatively stagnant waters sampled along the main river (9.2%). Based on relative abundance of Chl b, Chl c, fucoxanthin, peridinin, alloxanthin, and zeaxanthin, various phytoplanktonic assemblages were evidenced in the Amazon River system. Branched fatty acids in the carbon range of 15–17 gave insight into bacterial signatures. They showed low microbial contribution to the fatty acid pool, with slightest higher contribution in a swamp of stagnant waters and in the White waters of the Solimoes River.     

Microsatellite loci for two East African tree species, Leptonychia usambarensis (Sterculiaceae) and Sorindeia madagascariensis (Anacardiaceae)

We isolated 20 trinucleotide microsatellites from two African tree species: Sorindeia madagascariensis (nine microsatellites) and Leptonychia usambarensis (11 microsatellites). Number of alleles ranged from three to seven in Sorindeia and two to 10 in Leptonychia. Observed heterozygosity ranged from 0.025 to 0.829 for Sorindeia and from 0.226 to 0.933 for Leptonychia. Two loci from each species departed from Hardy-Weinberg equilibrium. These microsatellite markers will be used to study how forest fragmentation affects pollination and seed dispersal processes of these tree species.     

A microbiological examination of the skin and vaginal mucus of Amazon River freshwater dolphins (Inia geoffrensis) in relation to an assessment of the physiological state of the animals]

There is a definite relation between the state of dolphin's health and the abundance of bacterial associations developing on the skin surface around the dorsal fin. The disease was accompanied by an increase in bacterium amount more than fourfold due to the enhancement of staphylococcus and pseudomonad number. The development of dystrophy in the animal resulted in a threefold decrease in bacterium number. Pseudomonas aeruginosa dominated in this case. In the vaginal mucose of female, the development of bacteria had an oscillatory character and was correlated with the dynamics of leukocyte number against the background of morphologically diverse epithelial cells discharged in different periods of observation. Periods of the abundant bacterium development were connected with the cyclic recurrence of sexual (estrous) processes in the female organism.     

Microsatellite primers for relatedness and population structure in great frigatebirds (Pelecaniformes: Fregatidae)

Eighteen moderately polymorphic microsatellite loci were isolated and characterized for great frigatebirds Fregata minor. Polymorphism for the 12 dinucleotide and six tetranucleotide markers was assessed in 23 birds from a Hawaii population. Allelic diversity ranged from two to 12 (mean 5.9), with observed heterozygosity from 0.304 to 0.956 (mean 0.637). Three loci showed homozygote excess, possibly due to null alleles. One additional pair of loci exhibited strong gametic disequilibrium. Thus, at least 14 loci will be useful for studies of relatedness and population structure.     

Light and ultrastructural description of Meglitschia mylei n. sp. (myxozoa) from Myleus rubripinnis (Teleostei: Serrasalmidae) in the Amazon River system

Meglitschia mylei n. sp. found in the gall bladder of the teleostean fish Myleus rubripinnis (Serrasalmidae) from the middle Amazonian region of Brazil is described using light and transmission electron microscopy. The spores observed in the bile averaged 24.6±0.8 μm long, 8.7±0.4 μm wide and 5.1±0.3 μm thick and were strongly furcate and arcuate ∩-shaped composed of two symmetric equal-sized valves, up to ～70 nm thick. Each valve possessed one opposed tapering appendage, 20.1±0.7 μm long, oriented parallel towards the basal tip of the appendages and joined along a right suture line forming a thick strand. The strand goes around the central part of the spore, which in turn surrounds two equal and symmetric spherical polar capsules (PC), 2.1±0.3 μm in diameter, located at the same level. Each capsule contains a polar filament with five (rarely six) coils. The binucleate sporoplasm was irregular in shape, contained several sporoplasmosomes, ～175 nm in diameter and filled all the space of the two caudal appendages. Based on the arc shape of the spore with two tapering caudal appendages oriented to the basis of spores, on the number and position of the PC and of the polar filament coils and arrangements, and on the host specificity, we propose the name M. mylei n. sp. for this new myxozoan. Accordingly, this is the second described species of this genus.     

Microsatellite markers for identification and parentage analysis in the European wild boar (Sus scrofa)

ABSTRACT: BACKGROUND: The wild boar (Sus scrofa) is among the most widespread mammal species throughout the old world. Presently, studies concerning microsatellites in domestic pigs and wild boars have been carried out in order to investigate domestication, social behavior and general diversity patterns among either populations or breeds. The purpose of the current study is to develop a robust set of microsatellites markers for parentage analyses and individual identification. FINDINGS: A set of 14 previously reported microsatellites markers have been optimized and tested in three populations from Hungary, Portugal and Spain, in a total of 167 samples. The results indicate high probabilities of exclusion (0.99999), low probability of identity (2.0E-13 -- 2.5E-9) and a parentage assignment of 100%. CONCLUSIONS: Our results demonstrate that this set of markers is a useful and efficient tool for the individual identification and parentage assignment in wild boars.     

Community of parasites in Triportheus curtus and Triportheus angulatus (Characidae) from a tributary of the Amazon River system (Brazil)

The present study compared the community of parasites in populations of Triportheus angulatus and T. curtus from a tributary of the Amazon River in northern Brazil. All hosts had one or more parasite species, 862,687 parasites were collected from T. curtus and 302,008 from T. angulatus. Species richness of parasites, Shannon diversity index and evenness index were higher for T. angulatus. The parasite communities of both hosts was similar (99%) and composed by Ichthyophthirius multifiliis, Anacanthorus pitophallus, metacercariae and Procamallanus (Spirocamallanus) inopinatus, with dominance of I. multifiliis. However, low infection level by Piscinodinium pilullare, Dolops sp. and Contracaecum larvae occurred only in T. angulatus, and Spironucleus sp. was found only in T. curtus. There were differences in the prevalence, intensity and mean abundance for some parasites of both hosts. There was aggregated dispersion of parasites in both hosts, but the infection of P. (S.) inopinatus in T. angulatus showed a random dispersion. For T. angulatus and T. curtus, the diversity and abundance of parasites were influenced by the host size. This was the first report of these parasite species for T. curtus, as well as of I. multifiliis, P. pilullare, Dolops sp., P. (S.) inopinatus and Contracecum sp. for T. angulatus.     

Development and characterization of 30 polymorphic microsatellite markers for the Atlantic surfclam, Spisula solidissima (Dillwyn, 1817)

Thirty polymorphic microsatellite markers were developed for the Atlantic surfclam, Spisula solidissima, from an enriched library and characterized in 24 clams from a wild population. The number of alleles ranged from 3 to 16 per locus. The expected and observed heterozygosities ranged from 0.1942 to 0.9238 and 0.0833 to 0.875 respectively. Six loci showed significant (P < 0.05 after Bonferroni correction) deviation from Hardy–Weinberg equilibrium, probably because of the presence of null alleles. Three primer pairs amplified duplicated loci with two involving tandem mini‐satellite repeats. Most of the microsatellite markers developed here should be useful for genetic studies in this species.     

Isolation and characterization of microsatellite loci in Monolepta vincta Gerstaecker, 1871 (Coleoptera,Chrysomelidae, Galerucinae)

Nine polymorphic microsatellite markers of Monolepta vincta Gerstaecker, 1871 (Coleoptera, Chrysomelidae) have been characterized. An analysis of 140 individuals demonstrated the high degree of polymorphism for these loci with a mean number of 10.6 alleles per locus. Primer sets were also tested in M. usambarica Weise, 1903, M. vilis Weise, 1924 and an as yet undescribed Monolepta sp. Some primer sets yielded amplification products in these closely related species with a detectable degree of polymorphism. The markers will be used for a population genetic study of M. vincta populations in the Kakamega Forest, Kenya.     

Polymorphic heterologous microsatellite loci for population genetics studies of the white-faced ibis Plegadis chihi (Vieillot, 1817) (Pelecaniformes, Threskiornithidae)

We screened 44 heterologous microsatellites isolated in species of the families Threskiornithidae, Ciconiidae and Ardeidae for their use in a migratory waterbird, the white-faced ibis Plegadis chihi (Vieillot, 1817) (Threskiornithidae). Of the screened loci, 57% amplified successfully and 24% were polymorphic. In two breeding colonies from southern Brazil (N = 131) we detected 32 alleles (2-10 alleles/locus). Average He over all loci and colonies was 0.55, and the combined probability of excluding false parents, 98%. There was no departure from HWE in any loci or population. Eru6 and Eru4 loci were in non-random association in the Alvorada colony, and NnNF5 and Eru5 in both populations. AMOVA analysis indicated that most of the genetic diversity was contained within populations. Structure analysis suggested a single population, and F(ST) value showed weak genetic structuring (F(ST) = 0.009, p = 0.05). The two populations are apparently connected through gene-flow. The panel of six microsatellites optimized here was sufficiently informative for characterizing the genetic diversity and structure in these natural populations of the white-faced ibis. The information generated could be useful in future studies of genetic diversity, relatedness and the mating system in Plegadis chihi and related species.     

A new species of Notodiaptomus Kiefer, 1936 (Copepoda,Diaptomidae) from the Amazon and Orinoco River Basins

A new species of Notodiaptomus, Notodiaptomus simillimus sp. nov., based on the female originally but erroneously assigned to Rhacodiaptomus calatus, and the corresponding newly discovered male, is described and illustrated in detail. The designation of the female as a new species of Notodiaptomus, and the recognition of the corresponding new male, is based on detailed morphological and biometrical studies, analysis of the known distribution and material from laboratory cultures. Morphological analysis demonstrated that the female shares the form of the external genital area and setal armature of the exopod 2 of leg 5 with other species of Notodiaptomus but they differ from those exhibited by species of Rhacodiaptomus. The distributions of the female and male assigned to Notodiaptomus simillimus sp. nov. overlap and include the Atabapo and Guaviare Rivers and Lago Calado. On the other hand, the distributions of the males and females originally assigned to R. calatus are disjunct and where they overlap, that is, in Lago Calado, each is accompanied by its respective mate. Laboratory cultures showed that, as expected, copulation did not occur between males and females described originally as R. calatus. This experiment demonstrated the existence of reproductive isolating mechanisms between these females and males, and confirmed the existence of two distinct genetic pools, i.e. two different species, the original males being of the valid R. calatus and the female a new Notodiaptomus. This female and the corresponding newly discovered male are N. simillimus. The new species is closely related to N. coniferoides.     

Polymorphic microsatellite loci to study population dynamics in a dragonfly,the libellulid Trithemis arteriosa (Burmeister, 1839)

One of the most widely distributed dragonfly species in Africa is the red‐veined‐dropwing Trithemis arteriosa. It is an indicator for permanent water bodies, which are freshwater ecosystems of high environmental value especially in arid regions. For studies to determine population structures, assess species viability and monitor environmental changes, a panel of 10 polymorphic microsatellite loci was developed. The number of alleles per locus ranged from four to 12, with an observed heterozygosity ranging from 0.149 to 0.843.     

Microsatellite analysis of genetic population structure in an endangered salmonid: the coastal cutthroat trout (Oncorhynchus clarki clarki)

The genetic population structure of coastal cutthroat trout ( Oncorhynchus clarki clarki ) in Washington state was investigated by analysis of variation in allele frequencies at six highly polymorphic microsatellite loci for 13 anadromous populations, along with one outgroup population from the Yellowstone subspecies ( O. clarki bouvieri) (mean heterozygosity = 67%; average number of alleles per locus = 24). Tests for genetic differentiation revealed highly significant differences in genotypic frequencies for pairwise comparisons between all populations within geographical regions and overall population subdivision was substantial ( F _ST = 0.121, R _ST = 0.093), with 44.6% and 55.4% of the among-population diversity being attributable to differences between streams ( F _SR = 0.054) and between regions ( F _RT = 0.067), respectively. Analysis of genetic distances and geographical distances did not support a simple model of isolation by distance for these populations. With one exception, neighbour-joining dendrograms from the Cavalli-Sforza and Edwards' chord distances and maximum likelihood algorithms clustered populations by physiogeographic region, although overall bootstrap support was relatively low (53%). Our results suggest that coastal cutthroat trout populations are ultimately structured genetically at the level of individual streams. It appears that the dynamic balance between gene flow and genetic drift in the subspecies favours a high degree of genetic differentiation and population subdivision with the simultaneous maintenance of high heterozygosity levels within local populations. Results are discussed in terms of coastal cutthroat trout ecology along with implications for the designation of evolutionarily significant units pursuant to the US Endangered Species Act of 1973 and analogous conservation units.     

Isolation and characterization of microsatellite loci for the European tree frog (Hyla arborea)

We developed 11 new microsatellite markers for the European tree frog (Hyla arborea), and tested patterns of polymorphism in 54 adults (27 males and 27 females) from two ponds close to Lausanne (Western Switzerland). One marker was sex linked and two pairs displayed linkage disequilibrium. Comparisons of allele numbers with heterozygosity values support a stepwise-mutation model at neutral equilibrium, with mutation rates spanning nearly two orders of magnitude. These markers will prove useful for population genetic studies and fine-scale investigations requiring genetic assignment techniques.     

Development and characterization of microsatellite markers for the Amazonian blackwing hatchetfish,Carnegiella marthae (Teleostei,Gasteropelecidae)

The blackwing hatchetfish, Carnegiella marthae, is a small characin species distributed in forest streams of the Negro and upper Orinoco River basins in Amazonia. Freshwater hatchetfish are popular in the aquarium trade and represent an economic resource for the riverine people from middle Rio Negro, in Brazil. We isolated and characterized seven microsatellite DNA loci for the blackwing hatchetfish. Number of alleles and heterozygosity per locus in a sample of 30 fish ranged from three to 17 and from 0.19 to 0.87, respectively. These microsatellite loci provide powerful markers for studies on taxonomy, management and phylogeographic history of Amazonian hatchetfish.