Characterisation of microsatellite loci in the habitat-forming kelp, Ecklonia radiata (Phaeophyceae, Laminariales)

Habitat forming algae play an important role in the ecology of temperate reefs worldwide. Despite this, our understanding of levels of gene flow within and among populations of algae is largely limited to studies on intertidal species; we know comparatively little about important habitat-forming subtidal algae. Here, we develop eight polymorphic microsatellite markers for the characterisation of population genetic diversity and structure in the subtidal kelp, Ecklonia radiata. This large macroalga is the most abundant habitat-forming kelp on the subtidal rocky reefs of temperate Australia and New Zealand where it forms extensive forests that support an astounding diversity of associated taxa.     

Inter- and intraplant C-banding polymorphism in one population ofAegilops comosa subsp.comosa var.comosa (Poaceae)

The Giemsa C-banding pattern of the chromosomes of the native self-pollinatedAegilops comosa subsp.comosa var.comosa was studied. Six of the seven chromosomes of the haploid genome were found to be polymorphic for C-banding patterns. Chromosome A had four variants, chromosome E three variants and each of the chromosomes B, D, and F two variants. Chromosomes E and G were polymorphic for arm length and arm ratio.This paper is part of the doctoral dissertation ofA. Georgiou.     

Isolation and characterization of 12 novel microsatellite loci for the red panda (Ailurus fulgens)

The information on dispersal patterns and mating systems of red pandas is quite important for the understanding of the genetic diversity and divergence of this species. And microsatellite marker is an ideal tool to analyze dispersal patterns and mating systems. Thus, we describe in this paper the isolation and characterization of 12 microsatellite loci in the red panda from genomic DNA-enriched libraries. These loci were highly polymorphic with numbers of alleles per locus in 24 individuals ranging from 2 to 14, observed heterozygosity from 0.143 to 0.864 and expected heterozygosity from 0.297 to 0.872. All loci except for RP6 locus followed Hardy–Weinberg expectations. No significant linkage association was found among all these loci. The 12 novel polymorphic microsatellite loci will be of use in studying dispersal patterns and mating systems of red pandas.     

Standard karyotypes ofAegilops uniaristata,Ae. mutica,Ae. comosa subspeciescomosa andheldreichii (Poaceae)

C-banding patterns and polymorphisms were analyzed in several accessions of the diploidAegilops speciesAe. uniaristata, Ae. mutica, andAe. comosa subsp.comosa and subsp.heldreichii, and standard karyotypes of these species were established. Variation in C-band size and location was observed between different accessions, but did not prevent chromosome identification. One accession ofAe. uniaristata was homozygous for whole-arm translocations involving chromosomes 1N and 5N. The homoeologous relationships of these chromosomes were established by comparison of chromosome morphologies and C-banding patterns to other diploidAegilops species with known chromosome homoeology. In addition, in situ hybridization analysis with a 5S rDNA probe was used to identify homoeologous groups 1 and 5 chromosomes. The present analysis permitted the assignment of allAe. mutica, comosa subsp.comosa, andAe. comosa subsp.heldreichii chromosomes, and three of the sevenAe. uniaristata chromosomes according to their homoeologous groups. The data presented will be useful analyzing genome differentiation in polyploidAegilops species.     

Thirty-three microsatellite loci for noninvasive genetic studies of the giant panda (Ailuropoda melanoleuca)

Limited microsatellite markers useable in noninvasive genetic methods have hampered the studies of dispersal patterns and mating systems of giant pandas. Therefore, we describe in this paper the characterization of 15 novel microsatellite loci from genomic DNA-enriched libraries and 18 redesigned microsatellite loci from published papers on the giant panda. The number of alleles per locus in 60 individuals ranged from 2 to 13, the average observed heterozygosity per locus from 0.168 to 0.800, and the average expected heterozygosity per locus from 0.152 to 0.882. All loci followed Hardy-Weinberg expectations. Four pairs of significant linkage association were found among all these loci. Moreover, the 33 microsatellite loci showed high amplification successes rate in noninvasive samples, which indicated that these loci will be of use in studying dispersal patterns and mating systems of giant pandas using noninvasive genetic methods.     

Nine new microsatellite loci for the orange roughy (Hoplostethus atlanticus)

We isolated nine new dinucleotide microsatellites for the deep-sea fish Hoplostethus atlanticus. These loci are generally highly polymorphic, with allele number ranging from 3 to 31 and observed heterozygosity ranging from 0.067 to 0.933. In conjuction with previously published loci, these markers will be useful for fine-scale analysis of population structure in this commercially important and threatened species.     

Community effects following the deletion of a habitat-forming alga from rocky marine shores

Habitat-forming species increase spatial complexity and alter local environmental conditions, often facilitating a diversified assemblage of plants and animals. Removal of dominant species, therefore, can potentially lead to pronounced changes in diversity and community structure through a series of negative and positive interactions involving several components of the community. Here we test community responses to the deletion of the dominant, canopy-forming alga Hormosira banksii from the mid-intertidal zone of wave-protected rocky shores in southern New Zealand. This species was removed in winter (July) from three 3×3-m areas at each of two platforms (Kaikoura and Moeraki) on the east coast of the South Island. Initially, 59 taxa occurred in stands, but there were only four algal species with greater than 5% cover and three mobile invertebrate species with more than five individuals per 0.25 m². By 6 months after Hormosira removal, most fucoid and coralline algae had burned off, and there were blooms of ephemeral algae in the removal plots, but almost no change within controls. After 2 years, diversity declined by 44% relative to controls at Kaikoura and 36% at Moeraki, and the amount of bare space had increased by tenfold at Kaikoura and twofold at Moeraki. Few sessile or mobile invertebrates were present. Recruitment of Hormosira occurred after 14 months in the removal plots. At this time, a “press” disturbance was initiated into one half of each removal plot to test the effects of continued removal of Hormosira on diversity. Similar “end-points” of the control and “press” removal plots were not reached after 2 years, and even after Hormosira recruitment into the original “pulse” experiment there was little recovery of the community. In this mid-intertidal system with considerable thermal stress, and perhaps in others with few perennial species, diversity and community structure can critically depend on positive associations with a single dominant species.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Isolation and characterization of 18 microsatellite loci in the Egyptian vulture (Neophron percnopterus)

We developed 18 new microsatellite loci for the endangered Egyptian vulture (Neophron percnopterus). Microsatellite loci were screened for variation in two different populations belonging to separate subspecies: the nominal N. p. percnopterus and the Canarian N. p. majorensis. Mean expected heterosygosities were respectively 0.51 and 0.46, while the mean number of alleles per locus was 4.7 and 3.9. These new markers allow further genetic studies for the endangered Canarian Egyptian Vulture.     

Characterization of microsatellite loci in the marine seaweed Ascophyllum nodosum (Phaeophyceae; Fucales)

Ascophyllum nodosum L. dominates rocky intertidal shores throughout the temperate North Atlantic. Six microsatellite loci were developed for A. nodosum using enriched libraries. The number of alleles ranged from 9 to 24 and heterozygosities from 0.2213 to 0.7785. Ascophyllum is monotypic. There was no cross‐reactivity observed with Fucus serratus, F. vesiculosus or F. evanescens.     

Characterization of 22 microsatellite marker loci in the Madagascar rousette (Rousettus madagascariensis)

Twenty-two nuclear microsatellite loci were isolated from a genomic DNA library derived from Madagascar’s Rousettus madagascariensis. Marker characteristics were determined from a single population (37 individuals) from Fort Dauphin (southeastern Madagascar). Sixteen of the 22 loci were within Hardy–Weinberg expectations. These loci are highly informative with polymorphic information content values ranging between 0.757 and 0.916. These loci will provide valuable information for the study of population genetics and gene flow within this species of bats. Due to the dramatic reduction and alteration of their habitat, data generated utilizing this marker suite will potentially provide additional information for the effective long-term management of this near-threatened bat species.     

Isolation and characterization of 12 microsatellite loci from cutlassfish (Trichiurus haumela)

The cutlassfish (Trichiurus haumela) is an important commercial fish species. In the present study, we report 12 polymorphic microsatellite DNA markers for cutlassfish. The number of alleles per locus ranged from 2 to 9 in a sample of 26 individuals. Observed and expected heterozygosities per locus varied from 0.2727 to 0.9583 and from 0.4059 to 0.7926, respectively. Two loci (Trha25 and Trha27) showed significant departure from Hardy–Weinberg equilibrium after sequential Bonferroni correction (P < 0.0042). No significant linkage disequilibrium between pairs of loci was found. These microsatellite markers provide powerful tools for investigating genetic population structure, population history and conservation management of cutlassfish. Jin-Zhen Bi and Chang-Wei Shao contributed equally to this work.     

Characterization of 21 microsatellite marker loci in the silky sifaka (Propithecus candidus)

The silky sifaka, Propithecus candidus, considered one of the rarest and most endangered primates in the world, exists in only a few fragmented forests in northeastern Madagascar. This species faces increasing pressures as a direct result from loss of habitat in the form of tavy (slash and burn agriculture), illegal logging and mining along with hunting for subsistence, even within protected areas. We report a marker suite of 21 loci developed from genomic DNA from a silky sifaka collected in 2003 from Anjanaharibe-Sud Special Reserve. Polymorphism of each locus evaluated in 18 individuals pooled from Marojejy National Park and Anjanaharibe-Sud Special Reserve. The number of observed alleles per locus ranges from 2 to 7. The observed and expected heterozygosity were 0.389–0.889 and 0.322–0.789, respectively. The information revealed in this study will provide useful tools for further study of the social structure and population dynamics of the silky sifaka to facilitate conservation management in the imminent future.     

Electron and immunofluorescence microscopy on the fertilization ofFucus distichus (Fucales,Phaeophyceae)

Summary Processes of fertilization and zygote development inFucus distichus were studied by indirect immunofluorescence microscopy using anti- tubulin antibody and electron microscopy. Just after plasmogamy, sperm aster formation occurs during migration of a sperm nucleus toward an egg nucleus at the center of cytoplasm. Only sparse microtubules (MTs) exist around the egg nucleus. The sperm aster can be observed till karyogamy, but afterwards vanishes. Accompanying sperm aster formation, cortical MTs which are reticulately arranged develop further in the zygotes. In 4 h-old zygotes, characteristic structures which are composed of fine granular masses and consist of intermixed dense and lighter staining areas appear around the nucleus. These structures cannot be detected with anti- tubulin immunofluorescence microscopy. The two centrioles derived from the sperm separate and migrate to both poles. In 4 h-and 8 h-old zygotes, there are no defined MT foci around the zygote nucleus and MTs radiate from the circumference of it. In 12 h-old zygotes, each centriole has migrated to the poles and derivative centrioles are generated. The fine granular masses also migrate to both poles and finally disappear accompanying the appearance of numerous MTs radiating from the poles. Therefore, two distinct MT foci appear from 12 h onwards. Progressive stages of nuclear division were also examined with electron and immunofluorescence microscopy in 16 h-old zygotes. The sperm chloroplast with an eyespot and the sperm mitochondria with an intercristal tubular structure, which are distinctive from those of egg, can be detected after plasmogamy and karyogamy. The sperm chloroplast is still present in 16 h-old zygotes.     

Isolation and characterization of microsatellite loci in the red mangrove Rhizophora mangle (Rhizophoraceae) and its related species

Fourteen microsatellite markers were isolated from the red mangrove Rhizophora mangle (Rhizophoraceae), a widely distributed mangrove plant in the New World and West Africa. The range of expected heterozygosity of these markers was 0.000–0.672 in the two populations of R. mangle. Cross-species testing was examined for five other species of Rhizophora, and Kandelia candel and Bruguiera gymnorrhiza. All 14 markers could be amplified in R. samoensis, thirteen in R. racemosa, and six markers in all other species of Rhizophora. Our findings greatly increase the utility of these markers.     

Development and characterization of 13 novel microsatellite loci from the flat-headed bat (Tylonycteris pachypus) with cross-species amplification in closely related taxa

13 novel microsatellite loci was isolated using the enriched library method from genomic DNA of the flat-headed bat (Tylonycteris pachypus). These loci showed high levels of genetic polymorphism testing on 54 individuals sampled from Guangxi province, China. The number of observed alleles per locus ranged from 2 to 15. The expected and observed heterozygosity values ranged from 0.170 to 0.900 and from 0.185 to 0.944, respectively. One loci departed significantly from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction and no Linkage disequilibrium was found between any pairs of loci. In addition, these loci were tested in the sister species, Tylonycteris robustula, seven loci amplified successfully and were also polymorphic.     

Twelve novel polymorphic microsatellite loci for the Yellow grouper (Epinephelus awoara) and cross-species amplifications

Yellow grouper (Epinephelus awoara) is a commercially important marine fish species. A dinucleotide-enriched genomic library of E. awoara was constructed using the method of FIASCO. Twelve loci were polymorphic in a test population with alleles per locus ranging from two to eight, and observed and expected heterozygosities per locus from 0.13 to 1.00 and from 0.20 to 0.86, respectively. Five loci significantly deviated from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was found between pairs of loci. 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 diversity of E. awoara and related species. L. Zhao and C. Shao have contributed equally to this work.     

Characterization and multiplex genotyping of 16 polymorphic microsatellite loci in the endangered bumble-bee bat, Craseonycteris thonglongyai (Chiroptera: Craseonycteridae)

The bumble-bee bat (Craseonycteris thonglongyai) is an endangered species with a limited distribution range and a suspected declining population. Of the 30 microsatellites developed and tested in C. thonglongyai, 16 were amplified in two multiplex polymerase chain reactions (PCRs). Based on genotypes of 64 individuals from two populations, expected heterozygosities, averaged 0.50 in Myanmar and 0.61 in Thailand. Only one pair of loci showed linkage disequilibrium in one population and no deviation from Hardy–Weinberg equilibrium was detected. This set of 16 microsatellites will be useful to study population structure and gene flow in C. thonglongyai. Tin Nwe, retired.     

Eight microsatellite loci characterised in the European blackbird, Turdus merula

Although the European blackbird, Turdus merula, is one of the most abundant and conspicuous songbirds of the Western Palaearctic and, as such, has been subject of numerous behavioural and ecological studies, there is to date no specific, PCR-based marker system for this species, and information on the applicability of genetic markers from other species or genera is scant. Here, we report the successful amplification of eight microsatellite loci in the European blackbird. We compared levels of polymorphism between groups of individuals sampled during the breeding season at different geographic localities (Heligoland Island, North Sea and Radolfzell, south-western Germany). We found high levels of polymorphisms, which enabled us to ascertain population membership of individuals. The properties of the tested microsatellite markers make them suitable for population genetic studies as well as for kinship analyses.     

Isolation and characterization of microsatellite loci in Acer opalus (Aceraceae), a sexually-polymorphic tree, through an enriched genomic library

An enrichment protocol was used to isolate and characterize microsatellite loci in Acer opalus, a Mediterranean tree species. Highly polymorphic microsatellite loci were required for paternity analyses in a population of this species. Eight microsatellite loci were amplified and a total of 87 alleles were detected in a sample of 142 individuals from one population, allowing the identification of each individual with a unique multilocus genotype. The paternity exclusion probabilities varied from 0.261 for locus Aop820 to 0.806 for locus Aop450, and the parent-pair exclusion probabilities varied from 0.433 for Aop820 to 0.940 for Aop450. The cumulative probabilities of exclusion for paternity and parentage of the eight loci were both higher than 0.999, supporting the usefulness of these microsatellite loci for future paternity and parentage analyses in A. opalus. Cross-species transferability was also assayed, supporting their potential use in other eight Acer species.