MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics.

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

authors： Mason AS,Zhang J,Tollenaere R,Vasquez Teuber P,Dalton-Morgan J,Hu L,Yan G,Edwards D,Redden R,Batley J

更新日期：2015-09-01 00:00:00

abstract：:Streamlining the development and genotyping of microsatellites in species for which no genetic information is available represents an important technical challenge to overcome in order to enable mainstream application of state-of-the-art population genetic analysis techniques in nonmodel organisms. Using the example o...

journal_title：Molecular ecology resources

authors： Lepais O,Bacles CF

更新日期：2011-07-01 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

authors： Rodríguez-Ezpeleta N,Bradbury IR,Mendibil I,Álvarez P,Cotano U,Irigoien X

更新日期：2016-07-01 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

authors： Guillot G,Santos F

更新日期：2010-11-01 00:00:00

abstract：:The vast amount of phenotypic information collected in some wild animal populations makes them extremely valuable for unravelling the genetics of ecologically important traits and understanding how populations adapt to changes in their environment. Next generation sequencing has revolutionized the development of large...

journal_title：Molecular ecology resources

authors： Van Bers NE,Santure AW,Van Oers K,De Cauwer I,Dibbits BW,Mateman C,Crooijmans RP,Sheldon BC,Visser ME,Groenen MA,Slate J

更新日期：2012-07-01 00:00:00

abstract：:Microsatellite genotyping of hair and faeces using standard polymerase chain reaction (PCR) resulted in low success rates and high error rates in a 2003-2004 pilot study using noninvasive genetic sampling for the brown bear (Ursus arctos) in the Italian Alps. Thus, we evaluated the performance of multiplex pre-amplifi...

journal_title：Molecular ecology resources

authors： DE Barba M,Waits LP

更新日期：2010-07-01 00:00:00

abstract：:A variety of research projects focus on genetic variation among and within maternal lineages as encompassed by mitochondrial DNA (mtDNA). While mtDNA often differs substantially between species, large differences may also be found within species. The evaluation of such divergent lineages, for example in intraspecific ...

journal_title：Molecular ecology resources

authors： Lindell J,Murphy RW

更新日期：2008-01-01 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

authors： Pinosio S,González-Martínez SC,Bagnoli F,Cattonaro F,Grivet D,Marroni F,Lorenzo Z,Pausas JG,Verdú M,Vendramin GG

更新日期：2014-07-01 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

authors： Castoe TA,Poole AW,Gu W,Jason de Koning AP,Daza JM,Smith EN,Pollock DD

更新日期：2010-03-01 00:00:00

abstract：:Local adaptation is often studied via (i) multiple common garden experiments comparing performance of genotypes in different environments and (ii) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptat...

journal_title：Molecular ecology resources

authors： Lasky JR,Forester BR,Reimherr M

更新日期：2018-01-01 00:00:00

abstract：:Thirty-eight microsatellite loci were developed for the bird pollinated, autohexaploid, Eremophila glabra ssp. glabra. A genomic library was screened with dinucleotide and trinucleotide sequence repeats. Polymorphism ranged from one to 21 alleles per locus. Twenty-four loci exhibited null alleles, based on patterns of...

journal_title：Molecular ecology resources

authors： Elliott CP

更新日期：2009-07-01 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

authors： Nevill PG,Reed A,Bossinger G,Vaillancourt RE,Larcombe M,Ades PK

更新日期：2008-11-01 00:00:00

abstract：:GONe is a user-friendly, Windows-based program for estimating effective size (N(e) ) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele fr...

journal_title：Molecular ecology resources

authors： Coombs JA,Letcher BH,Nislow KH

更新日期：2012-01-01 00:00:00

abstract：:To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the techni...

journal_title：Molecular ecology resources

authors： Harrison JG,John Calder W,Shuman B,Alex Buerkle C

更新日期：2021-01-01 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

authors： Erickson KL,Pentico A,Quattrini AM,McFadden CS

更新日期：2021-01-01 00:00:00

abstract：:Rhizoprionodon lalandii and R. porosus are widely distributed along the Atlantic coast of the Americas, living close to coastal areas and therefore frequently captured by seaboard fisheries. However, morphological identification of species in this genus is very difficult, especially when sharks have their heads and fi...

journal_title：Molecular ecology resources

authors： Mendonça FF,Hashimoto DT,Porto-Foresti F,Oliveira C,Gadig OB,Foresti F

更新日期：2009-05-01 00:00:00

abstract：:Quantitative real-time PCR (qPCR) is slowly becoming established as a tool to quantify abundance of different arbuscular mycorrhizal fungal (AMF) taxa in roots and in soil. Here, we describe the development and field validation of qPCR markers (i.e. primers with associated hydrolysis probes), targeting taxon-specific ...

journal_title：Molecular ecology resources

authors： Thonar C,Erb A,Jansa J

更新日期：2012-03-01 00:00:00

abstract：:Noninvasive genetic sampling has increasingly been used in ecological and conservation studies during the last decade. A major part of the noninvasive genetic literature is dedicated to the search for optimal protocols, by comparing different methods of collection, preservation and extraction of DNA from noninvasive m...

journal_title：Molecular ecology resources

authors： Renan S,Speyer E,Shahar N,Gueta T,Templeton AR,Bar-David S

更新日期：2012-11-01 00:00:00

abstract：:High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry ...

journal_title：Molecular ecology resources

authors： Tedersoo L,Drenkhan R,Anslan S,Morales-Rodriguez C,Cleary M

更新日期：2019-01-01 00:00:00

abstract：:Solms-laubachia eurycarpa is a medicinal herb endemic to the Hengduan Mountains region of south-central China. We screened a partial genomic library enriched for microsatellites and characterized 10 polymorphic loci for S. eurycarpa. The number of alleles per locus ranged from five to 15, with an average of 9.6. The o...

journal_title：Molecular ecology resources

authors： Yue J,Feldheim KA,Sun H,Ree R

更新日期：2008-09-01 00:00:00

abstract：:Sequence-based specimen identification, known as DNA barcoding, is a common method complementing traditional morphology-based taxonomic assignments. The fundamental resource in DNA barcoding is the availability of a taxonomically reliable sequence database to use as a reference for sequence comparisons. Here, we provi...

journal_title：Molecular ecology resources

authors： Barco A,Raupach MJ,Laakmann S,Neumann H,Knebelsberger T

更新日期：2016-01-01 00:00:00

abstract：:This article documents the whole genome sequence information of the Indian Zaprionus indianus, a member of the fruit fly family Drosophilidae. The sequences were generated on an Illumina platform and reads and whole genome sequence submitted to NCBI to the SRA and BioProject databases, respectively. This is the first ...

journal_title：Molecular ecology resources

authors： Khanna R,Mohanty S

更新日期：2017-05-01 00:00:00

abstract：:Our understanding of Glossina fuscipes fuscipes, a major vector of sleeping sickness, has been severely constrained by a lack of genetic markers for mapping and population genetic studies. Here we present 10 newly developed microsatellite loci for this tsetse species. Heterozygosity levels in Moyo, an Ugandan populati...

journal_title：Molecular ecology resources

authors： Brown JE,Komatsu KJ,Abila PP,Robinson AS,Okedi LM,Dyer N,Donnelly MJ,Slotman MA,Caccone A

更新日期：2008-11-01 00:00:00

abstract：:The rice stem borer, Chilo suppressalis, is one of the most damaging insect pests to rice production worldwide. Although C. suppressalis has been the focus of numerous studies examining cold tolerance and diapause, plant-insect interactions, pesticide targets and resistance, and the development of RNAi-mediated pest m...

journal_title：Molecular ecology resources

authors： Ma W,Zhao X,Yin C,Jiang F,Du X,Chen T,Zhang Q,Qiu L,Xu H,Joe Hull J,Li G,Sung WK,Li F,Lin Y

更新日期：2020-01-01 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

authors： Hill CE,Tomko S,Hagen C,Schable NA,Glenn TC

更新日期：2008-01-01 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

authors： Giardina TJ,Clark AG,Fiumera AC

更新日期：2017-11-01 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

authors： Fan L,Hui JH,Yu ZG,Chu KH

更新日期：2014-07-01 00:00:00

abstract：:Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target-capture methods, using the previously designed arachnid-specific probe set, can target a maximum of about 1,000 loc...

journal_title：Molecular ecology resources

authors： Kulkarni S,Wood H,Lloyd M,Hormiga G

更新日期：2020-01-01 00:00:00

abstract：:A multiplex haplotype-specific polymerase chain reaction (MHS-PCR) method was developed, which identified seven Clupeiform species living in the tropical Eastern Atlantic region: Sardinella aurita, Sardinella maderensis, Ethmalosa fimbriata, Sardina pilchardus, Engraulis encrasicholus, Pellonula leonensis and Ilisha a...

journal_title：Molecular ecology resources

authors： Durand JD,Diatta MA,Diop K,Trape S

更新日期：2010-05-01 00:00:00

abstract：:Eight polymorphic microsatellites were isolated from the Greek smooth newt (Lissotriton vulgaris graecus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)(11) probe. The loci showed different variation patterns in a single breeding population (32 individuals) with mean nu...

journal_title：Molecular ecology resources

authors： Sotiropoulos K,Eleftherakos K,Tsaparis D,Kasapidis P,Magoulas A,Legakis A

更新日期：2009-01-01 00:00:00