![]() ![]() All computational steps are parallelized with Hadoop MapReduce and executed graphically with Cloudgene. The mtDNA-Server workflow includes parallel read alignment, heteroplasmy detection, artefact or contamination identification, variant annotation as well as several quality control metrics, often neglected in current mtDNA NGS studies. Here we present mtDNA-Server, a scalable web server for the analysis of mtDNA studies of any size with a special focus on usability as well as reliable identification and quantification of heteroplasmic variants. While several pipelines for analyzing heteroplasmies exist, issues in usability, accuracy of results and interpreting final data limit their usage. intra-individual sequence variation) to a higher level of detail. 5 Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria generation sequencing (NGS) allows investigating mitochondrial DNA (mtDNA) characteristics such as heteroplasmy (i.e.5 Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria PMC article.4 Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck 6020, Austria.3 Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor 48109, Michigan, USA.2 Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria.1 Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck 6020, Austria.We also report an extension to the species longevity from 2 to 4 years from genetic recaptures during our six-year study period. We conclude that the boundaries of drainages affect the White Mountains population structure but short, cryptic, overland paths among them likely play a role in replenishing genetic diversity. Our analysis led us to suspect fragmentation in its eastern fork, an area most impacted by human development. ![]() Analysis of mtDNA indicated that this was likely a long-term phenomenon, also suggesting that one of the watersheds (LCR) may have been more historically diverse than its contemporary snapshot (nuDNA). However, inferred clusters crossed watershed boundaries, and migration rates and dispersers suggest infrequent use of overland paths at nearby sub-drainages among each watershed. Both a priori and de novo structure supported stream-mediated gene flow. Using microsatellite and mtDNA, we examined the hypothesis of hydrologically-mediated gene flow (via riparian networks) by assessing structure, diversity, and the possibility of overland dispersal among disconnected watersheds (White Mountains, AZ). The New Mexico meadow jumping mouse ( Zapus hudsonius luteus) is Endangered due to a suite of disturbances to their riparian habitat but the degree of functional connectivity within and among the drainages they occupy is unknown. ![]() In the face of accelerated warming and drying, habitat specialists of riparian zones could be threatened with genetic erosion if their effective population sizes become small due to loss and fragmentation of habitat. ![]()
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