Abstract：
:The spatial signature of microevolutionary processes structuring genetic variation may play an important role in the detection of loci under selection. However, the spatial location of samples has not yet been used to quantify this. Here, we present a new two-step method of spatial outlier detection at the individual and deme levels using the power spectrum of Moran eigenvector maps (MEM). The MEM power spectrum quantifies how the variation in a variable, such as the frequency of an allele at a SNP locus, is distributed across a range of spatial scales defined by MEM spatial eigenvectors. The first step (Moran spectral outlier detection: MSOD) uses genetic and spatial information to identify outlier loci by their unusual power spectrum. The second step uses Moran spectral randomization (MSR) to test the association between outlier loci and environmental predictors, accounting for spatial autocorrelation. Using simulated data from two published papers, we tested this two-step method in different scenarios of landscape configuration, selection strength, dispersal capacity and sampling design. Under scenarios that included spatial structure, MSOD alone was sufficient to detect outlier loci at the individual and deme levels without the need for incorporating environmental predictors. Follow-up with MSR generally reduced (already low) false-positive rates, though in some cases led to a reduction in power. The results were surprisingly robust to differences in sample size and sampling design. Our method represents a new tool for detecting potential loci under selection with individual-based and population-based sampling by leveraging spatial information that has hitherto been neglected.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Wagner HH,Chávez-Pesqueira M,Forester BRdoi
10.1111/1755-0998.12653subject
Has Abstractpub_date
2017-11-01 00:00:00pages
1122-1135issue
6eissn
1755-098Xissn
1755-0998journal_volume
17pub_type
杂志文章abstract：:We describe the cloning and characterization of eight novel tetranucleotide microsatellite loci in the ornate chorus frog (Pseudacris ornata). We also screened 26 loci from GenBank that were isolated from other Pseudacris species and obtained consistent product from five of these dinucleotide loci. All loci are polymo...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02478.x
更新日期：2009-03-01 00:00:00
abstract：:Genomic technologies continue to shed light on important ecological and evolutionary questions. Nonetheless, these new tools are applied disproportionately in a small fraction of global biodiversity, partly because of technical challenges to studying highly diverse taxa that occur in low abundances in an environment (...
journal_title：Molecular ecology resources
pub_type： 新闻
doi：10.1111/1755-0998.13122
更新日期：2020-01-01 00:00:00
abstract：:Restriction-site-associated DNA sequencing (RAD-seq) and related methods are revolutionizing the field of population genomics in nonmodel organisms as they allow generating an unprecedented number of single nucleotide polymorphisms (SNPs) even when no genomic information is available. Yet, RAD-seq data analyses rely o...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12518
更新日期：2016-07-01 00:00:00
abstract：:Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccura...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13130
更新日期：2020-09-01 00:00:00
abstract：:Data on hundreds or thousands of single nucleotide polymorphisms (SNPs) provide detailed information about the relationships between individuals, but currently few tools can turn this information into a multigenerational pedigree. I present the r package sequoia, which assigns parents, clusters half-siblings sharing a...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12665
更新日期：2017-09-01 00:00:00
abstract：:The three-toed sloths (Bradypus) are slow-moving arboreal neotropical mammals. Understanding demographic variables (such as sex ratio) of populations is a key for conservation purposes. Nevertheless, gender assignment of Bradypus is particularly challenging because of the lack of sexual dimorphism in infants and in ad...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02820.x
更新日期：2010-07-01 00:00:00
abstract：:Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2010.02855.x
更新日期：2010-11-01 00:00:00
abstract：:Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are ...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13131
更新日期：2020-03-01 00:00:00
abstract：:The emu (Dromaius novaehollandiae), a member of ratite family, is native to Australia and has been introduced to other countries worldwide. In this work, 10 polymorphic microsatellite loci were isolated and characterized for emu from public sequences. Polymorphism was surveyed in 22 individuals from two different popu...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02315.x
更新日期：2008-11-01 00:00:00
abstract：:Single nucleotide polymorphism (SNP) markers were identified and validated for two stingrays species, Potamotrygon motoro and Potamotrygon falkneri, using double digest restriction-site associated DNA (ddRAD) reads using 454-Roche technology. A total of 226 774 reads (65.5 Mb) were obtained (mean read length 289 ± 183...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12564
更新日期：2017-05-01 00:00:00
abstract：:We developed 16 microsatellite markers in Cordia bifurcata, a Central and South American shrub. The markers show low polymorphism in C. bifurcata, a species suspected of self-fertilization or apomixis. Of four polymorphic loci, three had only two alleles. However, current research indicates that these markers hold val...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02131.x
更新日期：2008-09-01 00:00:00
abstract：:We describe 15 polymorphic microsatellite loci from the white-ruffed manakin Corapipo altera, a common understory bird of Neotropical lowland and montane evergreen forests from eastern Honduras to northwestern Colombia. These markers were developed in order to assess population structure and genetic diversity in a fra...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1471-8286.2007.01929.x
更新日期：2008-01-01 00:00:00
abstract：:Pedigree reconstruction using genotypic markers has become an important tool for the study of natural populations. The nonstandard nature of the underlying statistical problems has led to the necessity of developing specialized statistical and computational methods. In this article, a new version of pedigree reconstru...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2011.03061.x
更新日期：2012-01-01 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：:We isolated 18 microsatellites from Sycoscapter australis, a nonpollinating fig wasp that develops in figs of Ficus macrophylla, and assessed their variability in 20 wasps. We further optimized nine of these loci for use in three other Sycoscapter species that develop in Ficus rubiginosa figs and assessed their variab...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02284.x
更新日期：2009-05-01 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：:We report the characterization of eight microsatellite markers in the big-headed ant Pheidole megacephala, a pest ant registered in the list of '100 of the world's worst invasive alien species'. An enrichment protocol was used to isolate microsatellite loci, and polymorphism was explored with 36 individuals collected ...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02116.x
更新日期：2008-07-01 00:00:00
abstract：:Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are o...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12474
更新日期：2016-03-01 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：:Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12379
更新日期：2015-09-01 00:00:00
abstract：:Collectively called zooxanthellae, photosynthetic dinoflagellates in the family Symbiodiniaceae are typical endosymbionts that unequivocally mediate coral responses to environmental changes. Symbiodiniaceae are genetically diverse, encompassing at least nine phylogenetically distinct genera (clades A-I). The ribosomal...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13250
更新日期：2021-01-01 00:00:00
abstract：:DNA barcoding has become an important current scientific trend to the understanding of the world biodiversity. In the case of mega-diverse hot spots like Mexico, this technique represents an important tool for taxonomists, allowing them to concentrate in highlighted species by the barcodes instead of analyzing entire ...
journal_title：Molecular ecology resources
pub_type：
doi：10.1111/1755-0998.12149
更新日期：2013-11-01 00:00:00
abstract：:Long columns of migrating larval sciarid armyworms were discovered in central and northern Japan, specifically Kanagawa, Gunma, Miyagi and Akita prefectures, as well as Hokkaido. This is the first examination of armyworms in East Asia. In Europe, armyworms have been identified as Sciara militaris, belonging to the fam...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2011.03040.x
更新日期：2011-11-01 00:00:00
abstract：:Betel nut (Areca nut, Areca catechu L.) is a conspicuous and important cultivated plant of tropical and subtropical habitats throughout Southeast Asia and Oceania. As a significant cultural and social offering, the migration of betel nut associated with human dispersal is an important issue in ethnobotany and anthropo...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02504.x
更新日期：2009-03-01 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：:We developed a total of 50 microsatellite markers for the three fungal pathogens causing the most important leaf spot diseases of banana: 32 loci for Mycosphaerella fijiensis are presented, and nine loci each for Mycosphaerella musicola and Mycosphaerella eumusae. All these loci were polymorphic within each species on...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02180.x
更新日期：2008-09-01 00:00:00
abstract：:A microsatellite-enriched genomic library was obtained for the endangered Japanese loach Leptobotia curta, and 39 dinucleotide markers were successfully isolated and characterized. These markers had between one and nine alleles, with expected heterozygosity ranging from 0 to 0.839, in a population from the Lake Biwa-Y...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1471-8286.2007.01902.x
更新日期：2008-01-01 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：:The ability to detect the identity of a sample obtained from its environment is a cornerstone of molecular ecological research. Thanks to the falling price of shotgun sequencing, genome skimming, the acquisition of short reads spread across the genome at low coverage, is emerging as an alternative to traditional barco...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13135
更新日期：2020-05-01 00:00:00
abstract：:This article documents the public availability of (i) microbiomes in diet and gut of larvae from the dipteran Dilophus febrilis using massive parallel sequencing, (ii) SNP and SSR discovery and characterization in the transcriptome of the Atlantic mackerel (Scomber scombrus, L) and (iii) assembled transcriptome for an...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12454
更新日期：2015-11-01 00:00:00
