Molecular Ecology Resources

Publisher: Blackwell Publishing


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    Molecular ecology resources (Online)
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Blackwell Publishing

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Publications in this journal

  • Shawn Narum, Tim Vines, Jennifer Gow
    Molecular Ecology Resources 01/2015; 15(1).
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    ABSTRACT: Estimates of relatedness coefficients, based on genetic marker data, are often necessary for studies of genetics and ecology. While many estimates based on method-of-moment or maximum-likelihood methods exist for diploid organisms, no such estimators exist for organisms with multiple ploidy levels, which occur in some insect and plant species. Here, we extend five estimators to account for different levels of ploidy: one relatedness coefficient estimator, three coefficient of coancestry estimators, and one maximum-likelihood estimator. We use arrhenotoky (when unfertilized eggs develop into haploid males) as an example in evaluations of estimator performance by Monte-Carlo simulation. Also, three virtual sex-determination systems are simulated to evaluate their performances for higher levels of ploidy. Additionally, we used two real datasets to test the robustness of these estimators under actual conditions. We make available a software package, PolyRelatedness, for other researchers to apply to organisms that have various levels of ploidy.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 12/2014;
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    ABSTRACT: Digeneans and cestodes are species-rich taxa and can seriously impact human health, fisheries, aqua- and agriculture, and wildlife conservation and management. DNA barcoding using the COI Folmer region could be applied for species detection and identification, but both ‘universal’ and taxon-specific COI primers fail to amplify in many flatworm taxa. We found that high levels of nucleotide variation at priming sites made it unrealistic to design primers targeting all flatworms. We developed new degenerate primers that enabled acquisition of the COI barcode region from 100% of specimens tested (n=46), representing 23 families of digeneans and 6 orders of cestodes. This high success rate represents an improvement over existing methods. Primers and methods provided here are critical pieces towards redressing the current paucity of COI barcodes for these taxa in public databases.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 12/2014;
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    ABSTRACT: The quantification of the biological diversity in environmental samples using high-throughput DNA sequencing is hindered by the PCR bias caused by variable primer-template mismatches of the individual species. In some dietary studies there is the added problem that samples are enriched with predator DNA, so often a predator specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could co-block non-target species to some degree. Here we accurately estimate the extent of the PCR-biases induced by universal and blocking primers on a mock community prepared with DNA of twelve species of terrestrial arthropods. We also compare universal and blocking primer biases with those induced by variable annealing temperature and number of PCR cycles. The results show that reads of all species were recovered after PCR-enrichment at our control conditions (no blocking oligonucleotide, 45°C annealing temperature and 40 cycles) and high-throughput sequencing. They also show that the four factors considered biased the final proportions of the species to some degree. Among these factors the number of primer-template mismatches of each species had a disproportionate effect (up to five orders of magnitude) on the amplification efficiency. In particular, the number of primer-template mismatches explained most of the variation (~3/4) of the amplification efficiency of the species. The effect of blocking oligonucleotide concentration on non-target species relative abundance was also significant, but less important (below one order of magnitude). Considering the results reported here, the quantitative potential of the technique is limited, and only qualitative results (the species list) are reliable, at least when targeting the barcoding COI region.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 12/2014;
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    ABSTRACT: A key strategy to reduce coral loss is the development of effective control method for the corallivorous crown-of-thorns sea star (Acanthaster planci), an omnipresent scourge and threat to the biodiversity of reefs in the Indo-Pacific region. Limited genetic resources are available for this highly fecund species. In the present study, we explored one aspect at the heart of A. planci outbreaks, the male reproductive system. Using high-throughput sequencing technology, we report for first time the production of a comprehensive transcriptomic dataset for the testes of A. placni that can aid in understanding the molecular mechanisms involved in A. planci spermatogenesis and fertilisation. Through de novo transcriptome sequencing, we produced 52,965,998 raw reads corresponding to 4.76 Gb clean read data. From this, 243,870 contigs were assembled with Trinity and used to construct 92,792 unigenes. Distinct genes were then annotated with Blastx yielding 30,810 unigenes above the cut-off e-value set at 10-5, with ESTscan database query analyses yielding up to 5,366 unigenes to known hits. The identification of genes directly involved in sperm development (DEAD-box family proteins), motility, fertilisation and signalling (Bindin/Speract receptor) are also discussed.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 12/2014;
  • Marko Mutanen, Mari Kekkonen, Sean W.J. Prosser, Paul D.N. Hebert, Lauri Kaila
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    ABSTRACT: Each holotype specimen provides the only objective link to a particular Linnean binomen. Sequence information from them is increasingly valuable due to the growing usage of DNA barcodes in taxonomy. Since type specimens are often old, it may only be possible to recover fragmentary sequence information from them. We tested the efficacy of short sequences from type specimens in the resolution of a challenging taxonomic puzzle: the Elachista dispunctella complex which includes 64 described species with minuscule morphological differences. We applied a multi-step procedure to resolve the taxonomy of this species complex. First, we sequenced a large number of newly-collected specimens and as many holotypes as possible. Second, we used all >400 bp barcodes to re-examine species boundaries. We employed three unsupervised methods (BIN, ABGD, GMYC) with specified criteria on how to handle discordant results, and examined diagnostic bases from each delineated putative species (OTUs). Third, we evaluated the morphological characters of each OTU. Finally, we associated short barcodes from types with the delineated OTUs. In this step, we employed various supervised methods, including distance-based, tree-based and character-based. We recovered 658 bp barcode sequences from 194 of 215 fresh specimens, and recovered an average of 141 bp from 33 of 42 holotypes. We observed strong congruence among all methods and good correspondence with morphology. We demonstrate potential pitfalls with tree-, distance-, and character-based approaches when associating sequences of varied length. Our results suggest that sequences as short as 56 bp can often provide valuable taxonomic information. The results support significant taxonomic oversplitting of species in the Elachista dispunctella complex.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 12/2014;
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    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 non-model organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing errors. Here, we analyze data used to develop 4723 novel SNPs for the commercially important deep-sea fish, orange roughy (Hoplostethus atlanticus), in order to measure the impact of not accounting for systematic sequencing errors when filtering identified polymorphisms to be added to the SNP chip. We used SAMtools to identify polymorphisms in a Velvet assembly of genomic DNA sequence data from seven individuals. The resulting set of polymorphisms were filtered to minimise ‘bycatch’ – polymorphisms caused by sequencing or assembly error. An Illumina Infinium SNP chip was used to genotype a final set of 7,714 polymorphisms across 1,734 individuals. Five predictors of SNP validity were examined for their effect on the probability of obtaining an assayable SNP: depth of coverage, number of reads that support a variant, polymorphism type (e.g., A/C), strand-bias, and SNP probe design score. Our results support a strategy of filtering out systematic sequencing errors in order to improve the efficiency of SNP discovery. We show that blastx can be used as an efficient tool to identify single-copy genomic regions in the absence of a reference genome. The results have implications for research aiming to identify SNPs and build SNP genotyping assays for non-model organisms.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 11/2014;
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    ABSTRACT: In this study, we verified the power of DNA barcodes to discriminate Neotropical birds using Bayesian tree reconstructions of a total of 7,404 COI sequences from 1,521 species, including 55 Brazilian species with no previous barcode data. We found that 10.4% of species were non-monophyletic, most likely due to inaccurate taxonomy, incomplete lineage sorting, or hybridization. At least 0.5% of the sequences (2.5% of the sampled species) retrieved from GenBank were associated with database errors (poor quality sequences, NuMTs, misidentification or unnoticed hybridization). Paraphyletic species (5.8% of the total) can be related to rapid speciation events leading to non-reciprocal monophyly between recently diverged sister species, or to absence of synapormorphies in the small COI region analysed. We also performed two series of genetic distance calculations under the K2P model for intraspecific and interspecific comparisons: the first included all COI sequences, and the second included only monophyletic taxa observed in the Bayesian trees. As expected, the mean and median pairwise distances were smaller for intraspecific than for interspecific comparisons. However, there was no precise “barcode gap”, which was shown to be larger in the monophyletic taxon dataset than for the data from all species, as expected. Our results indicated that although database errors may explain some of the difficulties in the species discrimination of Neotropical birds, distance-based barcode assignment may also be compromised because of the high diversity of bird species and more complex speciation events in the Neotropics.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 11/2014;
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    ABSTRACT: Honeybee subspecies have been affected by human activities in Europe over the past few decades. One such example is the importation of non-local subspecies of bees which has had an adverse impacts on the geographical repartition and subsequently on the genetic diversity of the black honeybee Apis mellifera mellifera. In order to restore the original diversity of this local honeybee subspecies, different conservation centers were set up in Europe. In this study, we established a black honeybee conservation center Conservatoire de l'Abeille Noire d'Ile de France (CANIF) in the region of Ile-de-France, France. CANIF's honeybee colonies were intensively studied over a three-year period. This study included a drone congregation area (DCA) located in the conservation center. MtDNA COI-COII marker was used to evaluate the genetic diversity of CANIF's honeybee populations and the drones found and collected from the DCA. The same marker (mtDNA) was used to estimate the interactions and the haplotype frequency between CANIF's honeybee populations and ten surrounding honeybee apiaries located outside of the CANIF. Our results indicate that the colonies of the conservation center and the drones of the DCA show similar stable profiles compared to the surrounding populations with lower level of introgression. The mtDNA marker used on both DCA and colonies of the conservation center seems to be an efficient approach to monitor and maintain the genetic diversity of the protected honeybee populations.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 10/2014;
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    ABSTRACT: In this paper we describe the development and characterization of the first high density single nucleotide polymorphism (SNP) genotyping array for rainbow trout. The SNP array is publically available from a commercial vendor (Affymetrix). The SNP genotyping quality was high and validation rate was close to 90%. This is comparable to other farm animals and is much higher than previous smaller scale SNP validation studies in rainbow trout. High quality and integrity of the genotypes is evident from sample reproducibility and from nearly 100% agreement in genotyping results from other methods. The array is very useful for rainbow trout aquaculture populations with more than 40,900 polymorphic markers per population. For wild populations that were confounded by a smaller sample size the number of polymorphic markers was between 10,577 and 24,330. Comparison between genotypes from individual populations suggest good potential for identifying candidate markers for populations’ traceability. Linkage analysis and mapping of the SNPs to the reference genome assembly provide strong evidence for a wide distribution throughout the genome with good representation in all 29 chromosomes. A total of 68% of the genome scaffolds and contigs were anchored through linkage analysis using the SNP array genotypes, including ~20% of the genome assembly that has not been previously anchored to chromosomes.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 10/2014;
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    ABSTRACT: Single-nucleotide polymorphisms (SNPs) offer numerous advantages over anonymous markers such as microsatellites, including improved estimation of population parameters, finer-scale resolution of population structure, and more precise genomic dissection of quantitative traits. However, many SNPs are needed to equal the resolution of a single microsatellite, and reliable large-scale genotyping of SNPs remains a challenge in non-model species. Here, we document the creation of a 9K Illumina Infinium BeadChip for polar bears (Ursus maritimus), which will be used to investigate: 1) the fine-scale population structure among Canadian polar bears, and 2) the genomic architecture of phenotypic traits in the Western Hudson Bay subpopulation. To this end, we used restriction-site associated DNA (RAD) sequencing from 38 bears across their circumpolar range, as well as blood/fat transcriptome sequencing of 10 individuals from Western Hudson Bay. 6000 RAD SNPs and 3000 transcriptomic SNPs were selected for the chip, based primarily on genomic spacing and gene function respectively. Of the 9000 SNPs ordered from Illumina, 8042 were successfully printed, and—after genotyping 1450 polar bears—5441 of these SNPs were found to be well clustered and polymorphic. Using this array, we show rapid linkage disequilibrium decay among polar bears, we demonstrate that in a subsample of 78 individuals, our SNPs detect known genetic structure more clearly than 24 microsatellites genotyped for the same individuals, and that these results are not driven by the SNP ascertainment scheme. Here we present one of the first large-scale genotyping resources designed for a threatened species.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 09/2014;