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Molecular Ecology Resources

Petri Kemppainen, Arild Husby
Genome wide association studies have contributed immensely to our understanding of the genetic basis of complex traits. One major conclusion arising from these studies is that most traits are controlled by many loci of small effect, confirming the infinitesimal model of quantitative genetics. A popular approach to test for polygenic architecture involves so called 'chromosome partitioning' where phenotypic variance explained by each chromosome is regressed on the size of the chromosome. First developed for humans, this has now been repeatedly used in other species, but there has been no evaluation of the suitability of this method in species that can differ in their genome characteristics such as number and size of chromosomes...
March 14, 2018: Molecular Ecology Resources
Lauren K Lucas, Chris C Nice, Zachariah Gompert
Patterns of phenotypic variation within and among species can be shaped and constrained by trait genetic architecture. This is particularly true for complex traits, such as butterfly wing patterns, that consist of multiple elements. Understanding the genetics of complex trait variation across species boundaries is difficult, as it necessitates mapping in structured populations and can involve many loci with small or variable phenotypic effects. Here, we investigate the genetic architecture of complex wing pattern variation in Lycaeides butterflies as a case study of mapping multivariate traits in wild populations that include multiple nominal species or groups...
March 13, 2018: Molecular Ecology Resources
Neva Škrabar, Leslie M Turner, Luisa F Pallares, Bettina Harr, Diethard Tautz
Two subspecies of the house mouse, Mus musculus domesticus and Mus musculus musculus, meet in a narrow contact zone across Europe. Mice in the hybrid zone are highly admixed, representing the full range of mixed ancestry from the two subspecies. Given the distinct morphologies of these subspecies, these natural hybrids can be used for genome-wide association mapping at sufficiently high resolution to directly infer candidate genes. We focus here on limb bone length differences, which is of special interest for understanding the evolution of developmentally correlated traits...
March 9, 2018: Molecular Ecology Resources
Stefaniya Kamenova, Rebecca Mayer, Oskar R Rubbmark, Eric Coissac, Manuel Plantegenest, Michael Traugott
The rapidly growing field of molecular diet analysis is becoming increasingly popular among ecologists, especially when investigating methodologically challenging groups, such as invertebrate generalist predators. Prey DNA detection success is known to be affected by multiple factors, however, the type of dietary sample has rarely been considered. Here, we address this knowledge gap by comparing prey DNA detection success from three types of dietary samples. In a controlled feeding experiment, using the carabid beetle Pterostichus melanarius as a model predator, we collected regurgitates, feces and whole consumers (including their gut contents) at different time points post-feeding...
March 6, 2018: Molecular Ecology Resources
Marine S O Brieuc, Charles D Waters, Daniel P Drinan, Kerry A Naish
Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here we explore the use of Random Forest (RF), a powerful machine learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild or non-model organisms...
March 5, 2018: Molecular Ecology Resources
Derrick J Thrasher, Bronwyn G Butcher, Leonardo Campagna, Michael S Webster, Irby J Lovette
Information on genetic relationships among individuals is essential to many studies of the behavior and ecology of wild organisms. Parentage and relatedness assays based on large numbers of SNP loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150-600 after stringent filtering) from large numbers of individuals (up to 240 per run)...
February 17, 2018: Molecular Ecology Resources
Timothy J Divoll, Veronica A Brown, Jeff Kinne, Gary F McCracken, Joy M O'Keefe
Different second-generation sequencing technologies may have taxon-specific biases when DNA metabarcoding prey in predator feces. Our major objective was to examine differences in prey recovery from bat guano across two different sequencing workflows using the same fecal DNA extracts. We compared results between the Ion Torrent PGM and the Illumina MiSeq with similar library preparations and the same analysis pipeline. We focus on repeatability and provide an R Notebook in an effort toward transparency for future methodological improvements...
February 17, 2018: Molecular Ecology Resources
Anna Marcionetti, Victor Rossier, Joris A M Bertrand, Glenn Litsios, Nicolas Salamin
Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, principally known for their mutualistic interaction with sea anemones. They are characterized by particular life-history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare group to have experienced an adaptive radiation in the marine environment. Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus)...
February 17, 2018: Molecular Ecology Resources
Hui-Su Kim, Bo-Young Lee, Jeonghoon Han, Chang-Bum Jeong, Dae-Sik Hwang, Min-Chul Lee, Hye-Min Kang, Duck-Hyun Kim, Hee-Jin Kim, Spiros Papakostas, Steven A J Declerck, Ik-Young Choi, Atsushi Hagiwara, Heum Gi Park, Jae-Seong Lee
Monogononta is the most speciose class of rotifers, with more than 2000 species. The monogonont genus Brachionus is widely distributed at a global scale, and a few of its species are commonly used as ecological and evolutionary models to address questions related to aquatic ecology, cryptic speciation, evolutionary ecology, the evolution of sex, and ecotoxicology. With the importance of Brachionus species in many areas of research, it is remarkable that the genome has not been characterized. This study aims to address this lacuna by presenting, for the first time, the whole genome assembly of the freshwater species Brachionus calyciflorus...
February 16, 2018: Molecular Ecology Resources
Hui-Su Kim, Bo-Young Lee, Jeonghoon Han, Chang-Bum Jeong, Dae-Sik Hwang, Min-Chul Lee, Hye-Min Kang, Duck-Hyun Kim, Daehwan Lee, Jaebum Kim, Ik-Young Choi, Jae-Seong Lee
Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field-based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50=23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish, and zebrafish) were identified...
February 16, 2018: Molecular Ecology Resources
W Stovall, H R Taylor, M Black, S Grosser, K Rutherford, N J Gemmell
Establishing the sex of individuals in wild systems can be challenging and often requires genetic testing. Genotyping-by-sequencing (GBS) and other reduced-representation DNA sequencing (RRS) protocols (e.g., RADseq, ddRAD) have enabled the analysis of genetic data on an unprecedented scale. Here, we present a novel approach for the discovery and statistical validation of sex-specific loci in GBS datasets. We used GBS to genotype 166 New Zealand fur seals (NZFS, Arctocephalus forsteri) of known sex. We retained monomorphic loci as potential sex-specific markers in the locus discovery phase...
February 14, 2018: Molecular Ecology Resources
Ming-Bao Luan, Jian-Bo Jian, Ping Chen, Jun-Hui Chen, Jian-Hua Chen, Qiang Gao, Gang Gao, Ju-Hong Zhou, Kun-Mei Chen, Xuan-Min Guang, Ji-Kang Chen, Qian-Qian Zhang, Xiao-Fei Wang, Long Fang, Zhi-Min Sun, Ming-Zhou Bai, Xiao-Dong Fang, Shan-Cen Zhao, He-Ping Xiong, Chun-Ming Yu, Ai-Guo Zhu
Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fiber crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fiber quality, protein content, and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach...
February 8, 2018: Molecular Ecology Resources
Brian M Brost, Brittany A Mosher, Kristen A Davenport
Molecular techniques for detecting microorganisms, macroorganisms, and infectious agents are susceptible to false negative and false positive errors. If left unaddressed, these observational errors may yield misleading inference concerning occurrence, prevalence, sensitivity, specificity, and covariate relationships. Occupancy models are widely used to account for false negative errors, and more recently have even been used to address false positive errors, too. Current modeling options assume false positive errors only occur in truly negative samples, an assumption that yields biased inference concerning detection because a positive sample could be classified as such not because the target agent was successfully detected, but rather due to a false positive test result...
February 8, 2018: Molecular Ecology Resources
Gregory N Puncher, Alessia Cariani, Gregory E Maes, Jeroen Van Houdt, Koen Herten, Rita Cannas, Naiara Rodriguez-Ezpeleta, Aitor Albaina, M Andone Estonba, Molly Lutcavage, Alex Hanke, Jay Rooker, James S Franks, Joseph M Quattro, Gualtiero Basilone, Igaratza Fraile, Urtzi Laconcha, Nicolas Goñi, Ai Kimoto, A David Macías, Francisco Alemany, Simeon Deguara, Salem W Zgozi, Fulvio Garibaldi, Isik K Oray, F Saadet Karakulak, Noureddine Abid, Miguel N Santos, Piero Addis, Haritz Arrizabalaga, Fausto Tinti
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species' stock dynamics, a genome-wide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference...
February 6, 2018: Molecular Ecology Resources
Matthew B Hamilton, Maria Tartakovsky, Amy Battocletti
The genetic effective population size, Ne , can be estimated from the average gametic disequilibrium (r2^) between pairs of loci but such estimates require evaluation of assumptions and currently have few methods to estimate confidence intervals. SpEED-Ne is a suite of Matlab computer code functions to estimate Ne^ from r2^ with a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators. SpEED-Ne includes functions to either generate or input simulated genotype data to facilitate comparative studies of Ne^ estimators under various population genetic scenarios...
February 3, 2018: Molecular Ecology Resources
Syrie M Hermans, Hannah L Buckley, Gavin Lear
Using environmental DNA (eDNA) to assess the distribution of micro- and macro-organisms is becoming increasingly popular. However, the comparability and reliability of these studies is not well understood as we lack evidence on how different DNA extraction methods affect the detection of different organisms, and how this varies among sample types. Our aim was to quantify biases associated with six DNA extraction methods, and identify one which is optimal for eDNA research targeting multiple organisms and sample types...
February 2, 2018: Molecular Ecology Resources
Garrett J McKinney, Ryan K Waples, Carita E Pascal, Lisa W Seeb, James E Seeb
Whole genome duplications have occurred in the recent ancestors of many plants, fish, and amphibians. Signals of these whole genome duplications still exist in the form of paralogous loci. Recent advances have allowed reliable identification of paralogs in genotyping by sequencing (GBS) data such as that generated from restriction-site associated DNA sequencing (RADSeq); however, excluding paralogs from analyses is still routine due to difficulties in genotyping. This exclusion of paralogs may filter a large fraction of loci, including loci that may be adaptively important or informative for population genetic analyses...
February 2, 2018: Molecular Ecology Resources
Matthew G Bakker
Microbial ecology has been profoundly advanced by the ability to profile complex microbial communities by sequencing of marker genes amplified from environmental samples. However, inclusion of appropriate controls is vital to revealing the limitations and biases of this technique. 'Mock community' samples, in which the composition and relative abundances of community members are known, are particularly valuable for guiding library preparation and data processing decisions. I generated a set of three mock communities using 19 different fungal taxa, and demonstrate their utility by contrasting amplicon sequencing data obtained for the same communities under modifications to PCR conditions during library preparation...
February 1, 2018: Molecular Ecology Resources
Yanjun Zan, Örjan Carlborg
The adaptation to a new habitat often results in a confounding between genome-wide genotype and beneficial alleles. When the confounding is strong, or the allelic effects weak, it is a major statistical challenge to detect the adaptive polymorphisms. We describe a novel approach to dissect polygenic traits in natural populations. First, candidate adaptive loci are identified by screening for loci directly associated with the adaptive trait or the expression of genes known to affect it. Then, a multi-locus genetic architecture is inferred using a backward elimination association analysis across all candidate loci with an adaptive false discovery rate based threshold...
January 22, 2018: Molecular Ecology Resources
Joane S Elleouet, Sally N Aitken
Approximate Bayesian computation (ABC) is widely used to infer demographic history of populations and species using DNA markers. Genomic markers can now be developed for non-model species using reduced representation library (RRL) sequencing methods that select a fraction of the genome using targeted sequence capture or restriction enzymes (genotyping-by-sequencing, GBS). We explored the influence of marker number and length, knowledge of gametic phase, and tradeoffs between sample size and sequencing depth on the quality of demographic inferences performed with ABC...
January 22, 2018: Molecular Ecology Resources
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