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Molecular Ecology Resources

Thomas W A Braukmann, Natalia V Ivanova, Sean W J Prosser, Vasco Elbrecht, Dirk Steinke, Sujeevan Ratnasingham, Jeremy R deWaard, Jayme E Sones, Evgeny V Zakharov, Paul D N Hebert
Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways...
February 18, 2019: Molecular Ecology Resources
Alicia Grealy, Michael Bunce, Clare Holleley
Avian eggshell is a bio-ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historic populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more-diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40-60 year-old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterise the yield and quality of such DNA...
February 17, 2019: Molecular Ecology Resources
Kantima Thongjued, Wilaiwan Chotigeat, Sara Bumrungsri, Phuvadol Thanakiatkrai, Thitika Kitpipit
Insect DNA barcoding is a species identification technique used in biodiversity assessment and ecological studies. However, DNA extraction can result in the loss of up to 70% of DNA. Recent research has reported that direct PCR can overcome this issue. However, the success rates could still be improved, and tissues used for direct PCR could not be reused for further genetic studies. Here, we developed a direct PCR workflow that incorporates a 2-min sample preparation in PBS-buffer step for fast and effective universal insect species identification...
February 13, 2019: Molecular Ecology Resources
Astrid Cruaud, Sabine Nidelet, Pierre Arnal, Audrey Weber, Lucian Fusu, Alex Gumovsky, John Huber, Andrew Polaszek, Jean-Yves Rasplus
Target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as micro-arthropods can be challenging. Here, we propose easy to set up optimisations for DNA extraction and library preparation prior to target enrichment...
February 13, 2019: Molecular Ecology Resources
B C C Hume, E G Smith, M Ziegler, H J M Warrington, J A Burt, T C LaJeunesse, J Wiedenmann, C R Voolstra
We present SymPortal (, a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next-generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterise taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multi-copy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multi-copy nature is collapsed by analytical approaches thereby focusing on only the most abundant sequences...
February 11, 2019: Molecular Ecology Resources
Guangyi Fan, Yaolei Zhang, Xiaochuan Liu, Jiahao Wang, Zeguo Sun, Shuai Sun, He Zhang, Jianwei Chen, Meiqi Lv, Kai Han, Xiaoxuan Tan, Jie Hu, Rui Guan, Yuanyuan Fu, Shanshan Liu, Xi Chen, Qiwu Xu, Yating Qin, Longqi Liu, Jie Bai, Ou Wang, Jingbo Tang, Haorong Lu, Zhouchun Shang, Bo Wang, Guohai Hu, Xia Zhao, Yan Zou, Ao Chen, Meihua Gong, Wenwei Zhang, Simon Ming-Yuen Lee, Songhai Li, Junnian Liu, Zhen Li, Yishan Lu, Jamal S M Sabir, Mumdooh J Sabir, Muhummadh Khan, Nahid H Hajrah, Ye Yin, Karsten Kristiansen, Huanming Yang, Jian Wang, Xun Xu, Xin Liu
Marine mammals are important models for studying convergent evolution and aquatic adaption, thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome-level marine mammal genome assembly based on the data generated by the BGISEQ-500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of sperm whale including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparison with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation...
February 8, 2019: Molecular Ecology Resources
Robert M W Ferguson, Sonia Garcia-Alcega, Frederic Coulon, Alex J Dumbrell, Corinne Whitby, Ian Colbeck
Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry, and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardised methods for bioaerosol collection for molecular ecology research exist. Each study requires a process of optimisation, which greatly slows the advance of bioaerosol science...
February 8, 2019: Molecular Ecology Resources
Brian A Gill, Paul M Musili, Samson Kurukura, Abidikadir A Hassan, Jacob R Goheen, W John Kress, Maria Kuzmina, Robert M Pringle, Tyler R Kartzinel
Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA-barcode library for a savanna ecosystem in equatorial East Africa. We amassed up to five DNA barcode markers (rbcL, matK, trnL-F, trnH-psbA, and ITS) for 1,781 specimens representing up to 460 species (~92% of the known flora), increasing the number of plant DNA barcode records for Africa by ~9%...
January 31, 2019: Molecular Ecology Resources
Mariah H Meek, Wesley A Larson
The genomics revolution has initiated a new era of population genetics where genome-wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well-studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Here, amplicon sequencing refers to highly multiplexed PCR followed by high-throughput sequencing (e...
January 25, 2019: Molecular Ecology Resources
Romane H Cristescu, Russell L Miller, Anthony J Schultz, Lyndal Hulse, Damian Jaccoud, Stephen Johnston, Jon Hanger, Rosie Booth, Céline H Frère
Wildlife diseases are a recognized driver of global biodiversity loss, have substantial economic impacts, and are increasingly becoming a threat to human health. Disease surveillance is critical but remains difficult in the wild due to the substantial costs and potential biases associated with most disease detection methods. Non-invasive scat surveys have been proposed as a health monitoring methodology to overcome some of these limitations. Here, we use the known threat of Chlamydia disease to the iconic, yet vulnerable, koala Phascolarctos cinereus to compare three methods for Chlamydia detection in scats: multiplex quantitative PCR, next generation sequencing, and a detection dog specifically trained on scats from Chlamydia-infected koalas...
January 25, 2019: Molecular Ecology Resources
Elspeth A McLennan, Belinda R Wright, Katherine Belov, Carolyn J Hogg, Catherine E Grueber
Molecular markers are a useful tool allowing conservation and population managers to shed light on genetic processes affecting threatened populations. However, as technological advancements in molecular techniques continue to evolve, conservationists are frequently faced with new genetic markers, each with nuanced variation in their characteristics as well as advantages and disadvantages for informing various questions. We used a well-studied population of Tasmanian devils from Maria Island to illustrate the issues associated with combining multiple genetic datasets and to help answer a question posed by many population managers: which dataset will provide the most precise and accurate estimates of the population processes we are trying to measure? We analysed individual heterozygosity (as internal relatedness, IR) of 96 individuals, calculated using four genetic marker types (putatively neutral microsatellites, MHC-linked microsatellites, reduced representation sequencing, and candidate region resequencing)...
January 25, 2019: Molecular Ecology Resources
Jinliang Wang
Population genetics model based Bayesian methods have been proposed and widely applied to making unsupervised inference of population structure from a sample of multilocus genotypes. Usually they provide good estimates of the ancestry (or population membership) of sampled individuals by clustering them probabilistically or proportionally into (anonymous) populations. However, they have difficulties in accurately estimating the number of populations (K) represented by the sampled individuals. This study proposed a new ad hoc estimator of K, calculable from the output of a population clustering program such as STRUCTURE or ADMIXTURE...
January 25, 2019: Molecular Ecology Resources
Els Atema, Ellis Mulder, Arie J van Noordwijk, Simon Verhulst
Telomere length (TL) is increasingly used as a biomarker of senescence, but measuring telomeres remains a challenge. Within tissue samples, TL varies between cells and chromosomes. Class I telomeres are (presumably static) interstitial telomeric sequences, and terminal telomeres have been divided in shorter (Class II) telomeres and ultra-long (Class III) telomeres, and the presence of the latter varies strongly between species. Class II telomeres typically shorten with age, but little is known of Class III telomere dynamics...
January 23, 2019: Molecular Ecology Resources
Philipp Hermann, Angelika Heissl, Irene Tiemann-Boege, Andreas Futschik
As recombination plays an important role in evolution, its estimation and the identification of hotspot positions is of considerable interest. We propose a novel approach for estimating population recombination rates based on genotyping or sequence data that involves a sequential multiscale change point estimator. Our method also permits to take demography into account. It uses several summary statistics within a regression model fitted on suitable scenarios. Our proposed method is accurate, computationally fast, and provides a parsimonious solution by ensuring a type I error control against too many changes in the recombination rate...
January 21, 2019: Molecular Ecology Resources
Ethan Linck, C J Battey
One common method of minimizing errors in large DNA sequence datasets is to drop variable sites with a minor allele frequency below some specified threshold. Though widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little rigorous analysis. Here we use simulations and an empirical SNP dataset to demonstrate the impacts of minor allele frequency (MAF) thresholds on inference of population structure - often the first step in analysis of population genomic data...
January 19, 2019: Molecular Ecology Resources
Lauren C White, Claudia Fontsere, Esther Lizano, David A Hughes, Samuel Angedakin, Mimi Arandjelovic, Anne-Céline Granjon, Jörg B Hans, Jack D Lester, M Timothy Rabanus-Wallace, Carolyn Rowney, Veronika Städele, Tomas Marques-Bonet, Kevin E Langergraber, Linda Vigilant
Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although non-invasive samples, such as feces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA)...
January 14, 2019: Molecular Ecology Resources
Arnaud Becheler, Camille Coron, Stéphane Dupas
BACKGROUND: Genetic samples can be used to understand and predict the behavior of species living in a fragmented and temporally changing environment. To this aim, models of coalescence conditioned to environment through an explicit modeling of population growth and migration have been developed in the past years, and simulators implementing these models have been developed, enabling biologists to estimate parameters of interest with Approximate Bayesian Computation techniques. However, model choice is still limited, and developing new coalescence simulators is extremely time consuming because code reuse is limited...
January 14, 2019: Molecular Ecology Resources
Aude Rogivue, Rimjhim R Choudhury, Stefan Zoller, Stéphane Joost, François Felber, Michel Kasser, Christian Parisod, Felix Gugerli
Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i...
January 13, 2019: Molecular Ecology Resources
Vera M Warmuth, Hans Ellegren
Restriction-site associated DNA sequencing (RADSeq) facilitates rapid generation of thousands of genetic markers at relatively low cost; however, several sources of error specific to RADSeq methods often lead to biased estimates of allele frequencies and thereby to erroneous population genetic inference. Estimating the distribution of sample allele frequencies without calling genotypes was shown to improve population inference from whole genome sequencing data, but the ability of this approach to account for RADSeq-specific biases remains unexplored...
January 11, 2019: Molecular Ecology Resources
Oliver Manangwa, Thierry De Meeûs, Pascal Grébaut, Adeline Ségard, Mechtilda Byamungu, Sophie Ravel
Population genetics is a convenient tool to study the population biology of non-model and hard to sample species. This is particularly true for parasites and vectors. Heterozygote deficits and/or linkage disequilibrium often occur in such studies and detecting the origin of those (Wahlund effect, reproductive system or amplification problems) is uneasy. We used new tools (correlation between the number of times a locus is found in significant linkage disequilibrium and its genetic diversity, correlations between Wright's FIS and FST , FIS and number of missing data, FIT and allele size and standard errors comparisons) for the first time on a real data set of tsetse flies, a vector of dangerous diseases to humans and domestic animals in sub-Saharan Africa...
January 7, 2019: Molecular Ecology Resources
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