Abstract:
:Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark-recapture analyses. Deposition data were collected at five watering holes using sampling intervals of 1-7 days and averaged one pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA) degradation, 20 faecal samples were exposed to local environmental conditions and sampled at eight time points from one to 124 days. Average amplification success rates for six nDNA microsatellite loci were 81% for samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We evaluated the efficiency of different sampling intervals (1-10 days) by estimating the number of successful samples, success rate of individual identification and laboratory costs per successful sample. Cost per successful sample increased and success and efficiency declined as the sampling interval increased. Results indicate NDS of faecal pellets is a feasible method for individual identification, population estimation and demographic monitoring of Sonoran pronghorn. We recommend collecting samples <7 days old and estimate that a sampling interval of four to seven days in summer conditions (i.e., extreme heat and exposure to UV light) will achieve desired sample sizes for mark-recapture analysis while also maximizing efficiency [Corrected].
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Woodruff SP,Johnson TR,Waits LPdoi
10.1111/1755-0998.12362subject
Has Abstractpub_date
2015-07-01 00:00:00pages
843-54issue
4eissn
1755-098Xissn
1755-0998journal_volume
15pub_type
杂志文章abstract::Microsatellites are valuable markers for the analysis of genetic diversity, linkage mapping or genotyping. The limited availability of microsatellites for the genus Potentilla (Rosaceae) stipulated the isolation of markers from a representative (Potentilla pusilla Host) of the Potentilla core group that constitutes th...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03134.x
更新日期:2012-07-01 00:00:00
abstract::We report an accurate multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, capable of reproducing gene expression profiles from 16 target genes [12 genes of interest (GOIs) and four reference genes (RGs)] in Acropora millepora, a common reef-building model coral species. The 12 GOIs ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2010.02923.x
更新日期:2011-03-01 00:00:00
abstract::The herbaceous perennial Cirsium purpuratum is a pioneer on the southeast side of Mount Fuji in Japan. For genetic analysis of reproduction in this species, we developed polymorphic compound microsatellite markers using an adaptor-ligated library method and a simpler method called the intercompound microsatellite meth...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2007.02077.x
更新日期:2008-07-01 00:00:00
abstract::We report the development of 10 polymorphic molecular markers containing short tandem repeats in the cosmopolitan reef-building coral, Pocillopora damicornis, an important model species for coral health, physiology, ecology, and genetics. The availability of polymorphic DNA markers in P. damicornis can act as impetus ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.02017.x
更新日期:2008-05-01 00:00:00
abstract::Female Drosophila melanogaster frequently mate with multiple males in nature as shown through parentage analysis. Although polyandry is well documented, we know little about the timing between mating events in wild Drosophila populations due to the challenge of following behaviours of individual females. In this study...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12661
更新日期:2017-11-01 00:00:00
abstract::Two recent articles were written in response to our paper "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation." While we agree with some of the comments made by the authors of these two response papers, we still believe caution should be employed in RADseq stud...
journal_title:Molecular ecology resources
pub_type: 评论,信件
doi:10.1111/1755-0998.12677
更新日期:2017-05-01 00:00:00
abstract::Metabarcoding is increasingly used to assess species diversity by high-throughput sequencing where millions of sequences can be generated in parallel and multiple samples can be analysed in one sequencing run. Generating amplified fragments with a unique sequence identifier ('tag') for each sample is crucial, as it al...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13018
更新日期:2019-07-01 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::Although nematodes are one of the most diverse metazoan phyla, species identification through morphology is difficult. Several genetic markers have been used for their identification, but most do not provide species-level resolution in all groups, and those that do lack primer sets effective across the phylum, preclud...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12082
更新日期:2013-11-01 00:00:00
abstract::DNA extraction from minute hymenopterans and their larvae is difficult and challenging because of their small size indicating a low amount of starting material. Hence, 11 DNA extraction methods were compared to determine their efficacy in isolating DNA. Success of each method was scored on a 2% agarose gel after PCR o...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03074.x
更新日期:2012-01-01 00:00:00
abstract::To enable the accurate sexing of individuals of introduced populations of the small Indian mongoose, Herpestes auropunctatus, we designed a primer set for the amplification of the sex-specific fragments EIF2S3Y and EIF2S3X. Using this primer set, the expected amplification products were obtained for all samples of gen...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2010.02931.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::DNA-based methods have greatly enhanced the sensitivity and specificity of hematophagous arthropod bloodmeal identification. A variety of methods have been applied to study the blood-feeding behaviour of mosquitoes, ticks, black flies and other blood-feeding arthropods as it relates to host-parasite interactions and p...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02469.x
更新日期:2009-01-01 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::The interbreeding of individuals coming from genetically differentiated but incompletely isolated populations can lead to the formation of admixed populations, having important implications in ecology and evolution. In this simulation study, we evaluate how individual admixture proportions estimated by the software st...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13234
更新日期:2020-11-01 00:00:00
abstract::Proportional and separate models able to apply different combination of substitution rate matrix (SRM) and among-site rate variation model (ASRVM) to each locus are frequently used in phylogenetic studies of multilocus data. A proportional model assumes that branch lengths are proportional among partitions and a separ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03021.x
更新日期:2011-09-01 00:00:00
abstract::Recent advances in high-throughput sequencing technologies have offered the possibility to generate genomewide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters and to evaluate potential adaptive divergence. Here, we identified 27 556 single ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12476
更新日期:2016-05-01 00:00:00
abstract::Frequently, the diversity of umbrella taxa is invoked to predict patterns of other, less well-known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic diversity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining sampling efficiency...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02646.x
更新日期:2009-05-01 00:00:00
abstract::We combined restriction site associated DNA sequencing (RADseq) using a hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to develop molecular markers for the 16 gigabase genome of Cedrus atlantica, a conifer tree species. With each method, Illumina(®) reads from one individual were used to gener...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12329
更新日期:2015-05-01 00:00:00
abstract::Rhinobatos percellens, Rhinobatos horkelli and Zapteryx brevirostris, known as guitarfish, are commonly found inshore and caught by trawl nets. Recently, these species have been suffering sharp population declines. One of the main impediments to the development of conservation plans is the lack of information related ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02728.x
更新日期:2010-01-01 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::As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological varia...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13241
更新日期:2021-01-01 00:00:00
abstract::Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability of genomic resources for these species will be valuable in planning appropriate conservation measures. Whole-genome seq...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13233
更新日期:2020-11-01 00:00:00
abstract::DNA barcoding is a global initiative that provides a standardized and efficient tool to catalogue and inventory biodiversity, with significant conservation applications. Despite progress across taxonomic realms, globally threatened marine turtles remain underrepresented in this effort. To obtain DNA barcodes of marine...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02747.x
更新日期:2010-03-01 00:00:00
abstract::Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was a...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13291
更新日期:2020-11-05 00:00:00
abstract::Microsatellite loci were identified from the charcoal rot fungus (Macrophomina phaseolina). Primer pairs for 46 loci were developed, and of these, 13 were optimized and screened using genomic DNA from 55 fungal isolates collected predominantly from two soybean fields in Mississippi. Twelve of the optimized loci were p...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02511.x
更新日期:2009-05-01 00:00:00
abstract::Restriction fragment length polymorphism tools is an R application which supports a complete workflow of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), dealing with the problems which accompany analysis when PCR-RFLP is used in diversity studies. Large numbers of different RFLP samples ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12094
更新日期:2013-07-01 00:00:00
abstract::Interpretation of high-throughput sequence data requires an understanding of how decisions made during bioinformatic data processing can influence results. One source of bias that is often cited is PCR clones (or PCR duplicates). PCR clones are common in restriction site-associated sequencing (RAD-seq) data sets, whic...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13087
更新日期:2020-01-01 00:00:00
abstract::This article documents the addition of 153 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brassica oleracea, Brycon amazonicus, Dimorphandra wilsonii, Eupallasella percnurus, Helleborus foetidus, Ipomoea purpurea, Phrynops geoffroanus, Prochilodus...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12061
更新日期:2013-03-01 00:00:00
abstract::In order to facilitate the addition of a genetic component to conservation management plans for Georgia false indigo (Amorpha georgiana var. georgiana), a rare legume of the southeastern USA, 12 polymorphic microsatellite markers were developed. No gametic disequilibrium was detected among locus pairs, but observation...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02409.x
更新日期:2009-01-01 00:00:00