Abstract:
:In this article, we describe ednaoccupancy, an r package for fitting Bayesian, multiscale occupancy models. These models are appropriate for occupancy surveys that include three nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). ednaoccupancy allows users to specify and fit multiscale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model-selection criteria. We illustrate these features by analysing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Dorazio RM,Erickson RAdoi
10.1111/1755-0998.12735subject
Has Abstractpub_date
2018-03-01 00:00:00pages
368-380issue
2eissn
1755-098Xissn
1755-0998journal_volume
18pub_type
杂志文章abstract::The mitochondrial CO1 gene (cytochrome c oxidase I) is a widely accepted metazoan barcode region. In insects, the mitochondrial NADH dehydrogenase subunit 1 (ND1) gene region has proved to be another suitable marker especially for the identification of lower level taxonomic entities such as populations and sister spec...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12125
更新日期:2013-11-01 00:00:00
abstract::This study reports the isolation and characterization of 11 polymorphic microsatellites from a sand smelt (Atherina boyeri) genomic library. Enrichment was performed with di-, tri- and tetranucleotide motifs following the FIASCO procedure (fast isolation by AFLP of sequences containing repeats). All loci were found to...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02366.x
更新日期:2009-05-01 00:00:00
abstract::This study examined the interspecific amplification of nuclear microsatellite loci developed mainly for eucalypts in the subgenus Symphyomyrtus across five species within the second most speciose subgenus, subgenus Eucalyptus. A set of eight to 10 loci, depending on taxon, have been identified that are highly variable...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02362.x
更新日期:2008-11-01 00:00:00
abstract::Microsatellite loci were identified from Cornus kousa'National'. Primer pairs for 86 loci were developed and of these, eight were optimized and screened using genomic DNA from 22 kousa cultivars. All optimized loci were polymorphic and the number of alleles per locus ranged from three to 17. Observed heterozygosity ra...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2007.02062.x
更新日期:2008-07-01 00:00:00
abstract::sam is a Windows program designed to detect candidate loci for selection in whole-genome scans. It also gives valuable clues as regards the ecological factors at stake in the selection process. The method used is based on multiple univariate logistic regression models to test for association between allelic frequencie...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02162.x
更新日期:2008-09-01 00:00:00
abstract::Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2010.02965.x
更新日期:2011-03-01 00:00:00
abstract::Mosquitoes belonging to the Culex pipiens complex are primary vectors for diseases such as West Nile encephalitis, Eastern equine encephalitis, many arboviruses, as well as lymphatic filariases. Despite sharing physiological characteristics, each mosquito species within the Culex complex has unique behavioural and rep...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12083
更新日期:2013-05-01 00:00:00
abstract::Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic an...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02750.x
更新日期:2010-03-01 00:00:00
abstract::Global climate change (GCC) may be causing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by including intraspecific genetic structure and spatial autocorrelation ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13024
更新日期:2019-07-01 00:00:00
abstract::Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphid-parasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compare...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03083.x
更新日期:2012-03-01 00:00:00
abstract::We have developed eight high-quality microsatellite DNA loci for the saltmarsh sharp-tailed sparrow and one additional locus with evidence of null alleles. In a sample of 250-350 individuals, the average number of alleles per locus was 14.7 and average observed heterozygosity was 0.80. These loci were tested in three ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01885.x
更新日期:2008-01-01 00:00:00
abstract::Nematodes play an important role in ecosystem processes, yet the relevance of nematode species diversity to ecology is unknown. Because nematode identification of all individuals at the species level using standard techniques is difficult and time-consuming, nematode communities are not resolved down to the species le...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02611.x
更新日期:2009-11-01 00:00:00
abstract::Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morpholo...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12401
更新日期:2015-11-01 00:00:00
abstract::High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still poses notable challenges, especially for those working with organisms without ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12077
更新日期:2013-05-01 00:00:00
abstract::Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal mater...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12580
更新日期:2017-05-01 00:00:00
abstract::Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RA...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12404
更新日期:2015-11-01 00:00:00
abstract::We report results of cross-species amplification in Dactylis glomerata and Lolium perenne of 12 simple sequence repeats (SSRs) isolated from Lolium multiflorum×Festuca glaucescens, 42 SSRs from Festuca arundinacea and two sequence tagged sites from Oryza sativa. We compared the transferability and diversity between D....
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02168.x
更新日期:2009-01-01 00:00:00
abstract::Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the tran...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12232
更新日期:2014-07-01 00:00:00
abstract::We implemented multilocus selection in a spatially-explicit, individual-based framework that enables multivariate environmental gradients to drive selection in many loci as a new module for the landscape genetics programs, CDPOP and CDMetaPOP. Our module simulates multilocus selection using a linear additive model, pr...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13121
更新日期:2020-03-01 00:00:00
abstract::Asian arowana or dragonfish (Scleropages formosus) is an important fish species due to its unusual breeding biology and high economic value in the ornamental fish markets. In the present study, we aimed to (i) create the first transcriptome by Roche 454 pyrosequencing of Asian arowana brain and gonad samples; (ii) ide...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12212
更新日期:2014-05-01 00:00:00
abstract::DNA microarrays are a popular technique for the detection of microorganisms. Several approaches using specific oligomers targeting one or a few marker genes for each species have been proposed. Data analysis is usually limited to call a species present when its oligomer exceeds a certain intensity threshold. While thi...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02199.x
更新日期:2009-01-01 00:00:00
abstract::We developed four multiplex panels comprising 19 microsatellite loci and tested their amplification in 21 rodent species important for agricultural and conservation management (Microtus, Arvicola, Chionomys). On average, 17.6 loci amplified per species. Number of alleles ranged from 1 to 19 per locus. We report an add...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02521.x
更新日期:2009-05-01 00:00:00
abstract::The brushtail possum is a major agricultural and ecological pest in New Zealand. A novel noninvasive DNA sampling tool for detecting its presence (WaxTags, or WT) was tested. DNA was recovered from saliva left on WT, and two lengths (407 bp and 648 bp) of the cytochrome c oxidase I (COI) barcoding region were amplifie...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02498.x
更新日期:2009-03-01 00:00:00
abstract::We identified microsatellite sequences of potential utility in the house sparrow (Passer domesticus) and assigned their predicted genome locations. These sequences included newly isolated house sparrow loci, which we fully characterized. Many of the newly isolated loci were polymorphic in two other species of Passerid...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03115.x
更新日期:2012-05-01 00:00:00
abstract::We developed nine new nuclear dinucleotide microsatellite loci for Castor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cr...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02364.x
更新日期:2009-03-01 00:00:00
abstract::Many plants and some animal species are polyploids. Nondisomically inherited markers (e.g. microsatellites) in such species cannot be analysed directly by standard population genetics methods developed for diploid species. One solution is to transform the polyploid codominant genotypes to pseudodiploid-dominant genoty...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12210
更新日期:2014-05-01 00:00:00
abstract::Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of ha...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12235
更新日期:2014-07-01 00:00:00
abstract::The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how the computer program Geneland ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2010.02864.x
更新日期:2010-11-01 00:00:00
abstract::Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0-2000 m elevation contains at least 10 000 species of non-leaf-m...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02628.x
更新日期:2009-05-01 00:00:00
abstract::Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralog...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13287
更新日期:2020-10-21 00:00:00