当前位置： SCI文献检索 > Molecular Ecology Resources期刊下所有文献 > A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes.

A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes.

Abstract：

:Predicting whether a predator is capable of affecting the dynamics of a prey species in the field implies the analysis of the complete diet of the predator, not simply rates of predation on a target taxon. Here, we employed the Ion Torrent next-generation sequencing technology to investigate the diet of a generalist arthropod predator. A complete dietary analysis requires the use of general primers, but these will also amplify the predator unless suppressed using a blocking probe. However, blocking probes can potentially block other species, particularly if they are phylogenetically close. Here, we aimed to demonstrate that enough prey sequence could be obtained without blocking probes. In communities with many predators, this approach obviates the need to design and test numerous blocking primers, thus making analysis of complex community food webs a viable proposition. We applied this approach to the analysis of predation by the linyphiid spider Oedothorax fuscus in an arable field. We obtained over two million raw reads. After discarding the low-quality and predator reads, the libraries still contained over 61 000 prey reads (3% of the raw reads; 6% of reads passing quality control). The libraries were rich in Collembola, Lepidoptera, Diptera and Nematoda. They also contained sequences derived from several spider species and from horticultural pests (aphids). Oedothorax fuscus is common in UK cereal fields, and the results showed that it is exploiting a wide range of prey. Next-generation sequencing using general primers but without blocking probes provided ample sequences for analysis of the prey range of this spider and proved to be a simple and inexpensive approach.

journal_name

Mol Ecol Resour

journal_title

Molecular ecology resources

authors

Piñol J,San Andrés V,Clare EL,Mir G,Symondson WO

doi

10.1111/1755-0998.12156

subject

Has Abstract

pub_date

2014-01-01 00:00:00

pages

18-26

issue

1

eissn

1755-098X

issn

1755-0998

journal_volume

14

pub_type

杂志文章

相关文献

Molecular Ecology Resources文献大全
  • PERMANENT GENETIC RESOURCES: Isolation of 60 polymorphic microsatellite loci in EST libraries of four sibling species of the phytopathogenic fungal complex Microbotryum.

    abstract：:We report the development of 60 microsatellite markers on four species of the fungal complex Microbotryum, causing anther smut of the Caryophyllaceae. Microsatellites were found in four expressed sequence tag (EST) libraries, built from isolates of M. lychnis-dioicae, M. violaceum sensus stricto, M. lagerheimii and M....

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1471-8286.2007.01967.x

    authors： Giraud T,Yockteng R,Marthey S,Chiapello H,Jonot O,Lopez-Villavicencio M,DE Vienne DM,Hood ME,Refregier G,Gendrault-Jacquemard A,Wincker P,Dossat C

    更新日期：2008-03-01 00:00:00

  • Attack of the PCR clones: Rates of clonality have little effect on RAD-seq genotype calls.

    abstract：:Interpretation of high-throughput sequence data requires an understanding of how decisions made during bioinformatic data processing can influence results. One source of bias that is often cited is PCR clones (or PCR duplicates). PCR clones are common in restriction site-associated sequencing (RAD-seq) data sets, whic...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.13087

    authors： Euclide PT,McKinney GJ,Bootsma M,Tarsa C,Meek MH,Larson WA

    更新日期：2020-01-01 00:00:00

  • Permanent genetic resources added to molecular ecology resources database 1 October 2012-30 November 2012.

    abstract：:This article documents the addition of 153 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brassica oleracea, Brycon amazonicus, Dimorphandra wilsonii, Eupallasella percnurus, Helleborus foetidus, Ipomoea purpurea, Phrynops geoffroanus, Prochilodus...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12061

    authors： Molecular Ecology Resources Primer Development Consortium.,Aksoy S,Almeida-Val VM,Azevedo VC,Baucom R,Bazaga P,Beheregaray LB,Bennetzen JL,Brassaloti RA,Burgess TI,Caccone A,Chang SM,Ciampi AY,Ciancaleoni S,Clímaco GT,Cloue

    更新日期：2013-03-01 00:00:00

  • Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts.

    abstract：:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For nonmodel organisms with adaptive key innovations, patterns of regulatory evolution have been predominantly limited to targete...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12350

    authors： Kratochwil CF,Meyer A

    更新日期：2015-07-01 00:00:00

  • Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate.

    abstract：:Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02855.x

    authors： Sønstebø JH,Gielly L,Brysting AK,Elven R,Edwards M,Haile J,Willerslev E,Coissac E,Rioux D,Sannier J,Taberlet P,Brochmann C

    更新日期：2010-11-01 00:00:00

  • Cross-species amplification of Eucalyptus microsatellite loci.

    abstract：:This study examined the interspecific amplification of nuclear microsatellite loci developed mainly for eucalypts in the subgenus Symphyomyrtus across five species within the second most speciose subgenus, subgenus Eucalyptus. A set of eight to 10 loci, depending on taxon, have been identified that are highly variable...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2008.02362.x

    authors： Nevill PG,Reed A,Bossinger G,Vaillancourt RE,Larcombe M,Ades PK

    更新日期：2008-11-01 00:00:00

  • Microsatellite loci for dreissenid mussels (Mollusca: Bivalvia: Dreissenidae) and relatives: markers for assessing exotic and native populations.

    abstract：:We developed and tested 14 new polymorphic microsatellite loci for dreissenid mussels, including the two species that have invaded many freshwater habitats in Eurasia and North America, where they cause serious industrial fouling damage and ecological alterations. These new loci will aid our understanding of their gen...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2011.03012.x

    authors： Feldheim KA,Brown JE,Murphy DJ,Stepien CA

    更新日期：2011-07-01 00:00:00

  • Characterization of polymorphic microsatellite DNA markers in Hakea oldfieldii Benth. (Proteaceae).

    abstract：:A genomic library was constructed and 13 polymorphic microsatellite markers were developed for Hakea oldfieldii, a woody shrub endemic to southwest Western Australia. Polymorphism was investigated for these markers in 28 individuals from a single population located in restricted habitat at the base of the Whicher Rang...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2009.02616.x

    authors： Byrne M,Hankinson M

    更新日期：2009-07-01 00:00:00

  • A first step towards inferring levels of long-distance dispersal during past expansions.

    abstract：:Improving the realism of spatially explicit demographic models is important for better inferring the history of past populations and for understanding the genetic bases of adaptation and speciation. One particular type of demographic event to take into account is long-distance dispersal (LDD). The goals of this study ...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02881.x

    authors： Ray N,Excoffier L

    更新日期：2010-09-01 00:00:00

  • Isolation and characterization of microsatellite markers from the great hornbill, Buceros bicornis.

    abstract：:Thirteen polymorphic microsatellite markers were isolated and characterized from the great hornbill, Buceros bicornis. In analyses of 20 individuals, the numbers of alleles per locus varied from two to 11. The expected and observed heterozygosities ranged from 0.22 to 0.88 and from 0.20 to 1.00, respectively. The mean...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2008.02447.x

    authors： Chamutpong S,Saito DS,Viseshakul N,Nishiumi I,Poonswad P,Ponglikitmongkol M

    更新日期：2009-03-01 00:00:00

  • Using AFLP markers and the Geneland program for the inference of population genetic structure.

    abstract：:The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how the computer program Geneland ...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02864.x

    authors： Guillot G,Santos F

    更新日期：2010-11-01 00:00:00

  • Isolation, characterization and cross-species testing of microsatellites obtained from a sand smelt (Atherina boyeri) genomic library.

    abstract：:This study reports the isolation and characterization of 11 polymorphic microsatellites from a sand smelt (Atherina boyeri) genomic library. Enrichment was performed with di-, tri- and tetranucleotide motifs following the FIASCO procedure (fast isolation by AFLP of sequences containing repeats). All loci were found to...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2008.02366.x

    authors： Milana V,Sola L,Rossi AR,Barbisan F,Congiu L

    更新日期：2009-05-01 00:00:00

  • Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size.

    abstract：:The concept of effective population size (N(e) ) is based on an elegantly simple idea which, however, rapidly becomes very complex when applied to most real-world situations. In natural populations, spatial and temporal stratifications create different classes of individuals with different vital rates, and this in tur...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02876.x

    authors： Waples RS

    更新日期：2010-09-01 00:00:00

  • SNP discovery in nonmodel organisms: strand bias and base-substitution errors reduce conversion rates.

    abstract：:Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing error...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12343

    authors： Gonçalves da Silva A,Barendse W,Kijas JW,Barris WC,McWilliam S,Bunch RJ,McCullough R,Harrison B,Hoelzel AR,England PR

    更新日期：2015-07-01 00:00:00

  • Leader of the pack: faecal pellet deposition order impacts PCR amplification in wombats.

    abstract：:DNA sourced from faeces is notoriously less reliable than that from tissue. Hence, understanding whether faecal pellet quality varies within faecal piles may be important for sample selection. We hypothesized that the order in which faecal pellets are deposited may influence microsatellite polymerase chain reaction (P...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2009.02582.x

    authors： Walker FM,Horsup A,Taylor AC

    更新日期：2009-05-01 00:00:00

  • A combined parasitological molecular approach for noninvasive characterization of parasitic nematode communities in wild hosts.

    abstract：:Most hosts are concurrently or sequentially infected with multiple parasites; thus, fully understanding interactions between individual parasite species and their hosts depends on accurate characterization of the parasite community. For parasitic nematodes, noninvasive methods for obtaining quantitative, species-speci...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12382

    authors： Budischak SA,Hoberg EP,Abrams A,Jolles AE,Ezenwa VO

    更新日期：2015-09-01 00:00:00

  • Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data.

    abstract：:Proportional and separate models able to apply different combination of substitution rate matrix (SRM) and among-site rate variation model (ASRVM) to each locus are frequently used in phylogenetic studies of multilocus data. A proportional model assumes that branch lengths are proportional among partitions and a separ...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2011.03021.x

    authors： Tanabe AS

    更新日期：2011-09-01 00:00:00

  • Isolation and characterization of microsatellite markers from the white-ruffed manakin Corapipo altera (Aves, Pipridae).

    abstract：:We describe 15 polymorphic microsatellite loci from the white-ruffed manakin Corapipo altera, a common understory bird of Neotropical lowland and montane evergreen forests from eastern Honduras to northwestern Colombia. These markers were developed in order to assess population structure and genetic diversity in a fra...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1471-8286.2007.01929.x

    authors： Barnett JR,Stenzler LM,Ruiz-Gutierrez V,Bogdanowicz SM,Lovette IJ

    更新日期：2008-01-01 00:00:00

  • The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections.

    abstract：:Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccura...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.13130

    authors： Vershinina AO,Kapp JD,Baryshnikov GF,Shapiro B

    更新日期：2020-09-01 00:00:00

  • The quest for Y-chromosomal markers - methodological strategies for mammalian non-model organisms.

    abstract：:Tracing maternal and paternal lineages independently to explore breeding systems and dispersal strategies in natural populations has been high on the wish-list of evolutionary biologists. As males are the heterogametic sex in mammals, such sex-specific patterns can be indirectly observed when Y chromosome polymorphism...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2009.02798.x

    authors： Greminger MP,Krützen M,Schelling C,Pienkowska-Schelling A,Wandeler P

    更新日期：2010-05-01 00:00:00

  • Advancing ecological understandings through technological transformations in noninvasive genetics.

    abstract：:Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used fo...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2009.02699.x

    authors： Beja-Pereira A,Oliveira R,Alves PC,Schwartz MK,Luikart G

    更新日期：2009-09-01 00:00:00

  • MtDNA COI-COII marker and drone congregation area: an efficient method to establish and monitor honeybee (Apis mellifera L.) conservation centres.

    abstract：:Honeybee subspecies have been affected by human activities in Europe over the past few decades. One such example is the importation of nonlocal subspecies of bees which has had an adverse impact on the geographical repartition and subsequently on the genetic diversity of the black honeybee Apis mellifera mellifera. To...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12339

    authors： Bertrand B,Alburaki M,Legout H,Moulin S,Mougel F,Garnery L

    更新日期：2015-05-01 00:00:00

  • The first transcriptome and genetic linkage map for Asian arowana.

    abstract：:Asian arowana or dragonfish (Scleropages formosus) is an important fish species due to its unusual breeding biology and high economic value in the ornamental fish markets. In the present study, we aimed to (i) create the first transcriptome by Roche 454 pyrosequencing of Asian arowana brain and gonad samples; (ii) ide...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12212

    authors： Shen XY,Kwan HY,Thevasagayam NM,Prakki SR,Kuznetsova IS,Ngoh SY,Lim Z,Feng F,Chang A,Orbán L

    更新日期：2014-05-01 00:00:00

  • Isolation and characterization of 28 new microsatellite markers for European flounder (Platichthys flesus L.).

    abstract：:The European flounder (Platichthys flesus L.) is used in ecotoxicological studies to provide detailed information on the effects of pollution on individual fish. Data on population and evolutionary level effects are, however, limited. Here, the isolation and characterization of 28 novel species specific microsatellite...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2009.02589.x

    authors： Tysklind N,Neuparth T,Ashcroft GR,Taylor MI,Lyons BP,McCarthy ID,Carvalho GR

    更新日期：2009-05-01 00:00:00

  • Identification of the shark species Rhizoprionodon lalandii and R. porosus (Elasmobranchii, Carcharhinidae) by multiplex PCR and PCR-RFLP techniques.

    abstract：:Rhizoprionodon lalandii and R. porosus are widely distributed along the Atlantic coast of the Americas, living close to coastal areas and therefore frequently captured by seaboard fisheries. However, morphological identification of species in this genus is very difficult, especially when sharks have their heads and fi...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2009.02524.x

    authors： Mendonça FF,Hashimoto DT,Porto-Foresti F,Oliveira C,Gadig OB,Foresti F

    更新日期：2009-05-01 00:00:00

  • Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material.

    abstract：:Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal mater...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12580

    authors： Nielsen EE,Morgan JAT,Maher SL,Edson J,Gauthier M,Pepperell J,Holmes BJ,Bennett MB,Ovenden JR

    更新日期：2017-05-01 00:00:00

  • The quest for absolute abundance: The use of internal standards for DNA-based community ecology.

    abstract：:To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the techni...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章,评审

    doi：10.1111/1755-0998.13247

    authors： Harrison JG,John Calder W,Shuman B,Alex Buerkle C

    更新日期：2021-01-01 00:00:00

  • A primer set to determine sex in the small Indian mongoose, Herpestes auropunctatus.

    abstract：:To enable the accurate sexing of individuals of introduced populations of the small Indian mongoose, Herpestes auropunctatus, we designed a primer set for the amplification of the sex-specific fragments EIF2S3Y and EIF2S3X. Using this primer set, the expected amplification products were obtained for all samples of gen...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02931.x

    authors： Murata C,Ogura G,Kuroiwa A

    更新日期：2011-03-01 00:00:00

  • A multilocus, temperature stress-related gene expression profile assay in Acropora millepora, a dominant reef-building coral.

    abstract：:We report an accurate multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, capable of reproducing gene expression profiles from 16 target genes [12 genes of interest (GOIs) and four reference genes (RGs)] in Acropora millepora, a common reef-building model coral species. The 12 GOIs ...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/j.1755-0998.2010.02923.x

    authors： Souter P,Bay LK,Andreakis N,Császár N,Seneca FO,van Oppen MJ

    更新日期：2011-03-01 00:00:00

  • Characterization and analysis of a de novo transcriptome from the pygmy grasshopper Tetrix japonica.

    abstract：:The pygmy grasshopper Tetrix japonica is a common insect distributed throughout the world, and it has the potential for use in studies of body colour polymorphism, genomics and the biology of Tetrigoidea (Insecta: Orthoptera). However, limited biological information is available for this insect. Here, we conducted a d...

    journal_title：Molecular ecology resources

    pub_type： 杂志文章

    doi：10.1111/1755-0998.12553

    authors： Qiu Z,Liu F,Lu H,Huang Y

    更新日期：2017-05-01 00:00:00