Byers, Alexa K Condron, Leo O'Callaghan, Maureen Waipara, Nick Black, Amanda
Published in
Molecular ecology resources
Phytophthora agathidicida is a virulent soil pathogen of Aotearoa New Zealand's iconic kauri tree species (Agathis australis (D. Don) Lindl.) and the primary causal agent of kauri dieback disease. To date, only a few control options are available to treat infected kauri that are expressing symptoms of dieback disease. Previous research has identifi...
Thomas, Lemarcis Amandine, Blin Marie, Cariou Alessandro, Derzelle Sarah, Farhat Alexander, Fedosov Paul, Zaharias Dario, Zuccon Nicolas, Puillandre
Published in
Molecular ecology resources
The exon capture approach allows for sequencing a large number of loci to reconstruct phylogenetic relationships at varying taxonomic levels. In order to efficiently recover the targeted loci, the probes designed to capture the exons need to be genetically sufficiently similar to bind to the DNA, with a proposed limit of 10% of divergence. However,...
Forneris, Natalia Soledad Bosse, Mirte Gautier, Mathieu Druet, Tom
Published in
Molecular ecology resources
In populations of small effective size (Ne), such as those in conservation programmes, companion animals or livestock species, inbreeding control is essential. Homozygosity-by-descent (HBD) segments provide relevant information in that context, as they allow accurate estimation of the inbreeding coefficient, provide locus-specific information and t...
Blattner, Lucas André Lapellegerie, Pierre Courtney-Mustaphi, Colin Heiri, Oliver
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Molecular ecology resources
Chironomidae, so-called non-biting midges, are considered key bioindicators of aquatic ecosystem variability. Data derived from morphologically identifying their chitinous remains in sediments document chironomid larvae assemblages, which are studied to reconstruct ecosystem changes over time. Recent developments in sedimentary DNA (sedDNA) researc...
Zhao, Lei Henriksen, Rasmus Amund Ramsøe, Abigail Nielsen, Rasmus Korneliussen, Thorfinn Sand
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Molecular ecology resources
One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithrea...
Baeza, J Antonio Minish, Jeremiah J Michael, Todd P
Published in
Molecular ecology resources
Complete mitochondrial genomes have become markers of choice to explore phylogenetic relationships at multiple taxonomic levels and they are often assembled using whole genome short-read sequencing. Herein, using three species of sea chubs as an example, we explored the accuracy of mitochondrial chromosomes assembled using Oxford Nanopore Technolog...
Ruzzante, Daniel E McCracken, Gregory R Fraser, Dylan J MacMillan, John Buhariwalla, Colin Flemming, Joanna Mills
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Molecular ecology resources
Although efforts to estimate effective population size, census size and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how repeatable or representative many estimates may be. Answering this question requires studies of long-term population dynamics. Her...
Beemelmanns, Anne Bouchard, Raphaël Michaelides, Sozos Normandeau, Eric Jeon, Hyung-Bae Chamlian, Badrouyk Babin, Charles Hénault, Philippe Perrot, Océane Harris, Les N
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Molecular ecology resources
Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational and subsistence mixed-stock fisheries. Arctic Char (Salvelinus alpinus), Brook Trout (Salvelinus fontinalis) and Lake Whitefish (Coregonus clupeaformi...
Hiraoka, Satoshi Ijichi, Minoru Takeshima, Hirohiko Kumagai, Yohei Yang, Ching-Chia Makabe-Kobayashi, Yoko Fukuda, Hideki Yoshizawa, Susumu Iwasaki, Wataru Kogure, Kazuhiro
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Published in
Molecular ecology resources
The ammonia monooxygenase subunit A (amoA) gene has been used to investigate the phylogenetic diversity, spatial distribution and activity of ammonia-oxidising archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of amoA is a widely used method; however, it produces inac...
Wu, Ping Xue, Ningning Yang, Jie Zhang, Qiang Sun, Yuzhe Zhang, Wen
Published in
Molecular ecology resources
Organelle genomes serve as crucial datasets for investigating the genetics and evolution of plants and animals, genome diversity, and species identification. To enhance the collection, analysis, and visualisation of such data, we have developed a novel open-source software tool named Organelle Genome Utilities (OGU). The software encompasses three ...