Abstract:
:Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years; however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy next-generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this approach appear to be unaware that many single nucleotide polymorphisms (SNPs) identified from genome-wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses. Here, we demonstrate two methods for mining mitochondrial markers using RAD sequence data from three South African species of yellowfish, Labeobarbus. First, we use a rigorous SNP discovery pipeline using the program stacks, to identify variant sites in mtDNA, which we then combine into haplotypes. Second, we directly map sequence reads against a mitochondrial genome reference. This method allowed us to reconstruct up to 98% of the Labeobarbus mitogenome. We validated these mitogenome reconstructions through blast database searches and by comparison with cytochrome b gene sequences obtained through Sanger sequencing. Finally, we investigate the organismal consequences of these data including ancient genetic exchange and a recent translocation among populations of L. natalensis, as well as interspecific hybridization between L. aeneus and L. kimberleyensis.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Stobie CS,Cunningham MJ,Oosthuizen CJ,Bloomer Pdoi
10.1111/1755-0998.12953subject
Has Abstractpub_date
2019-01-01 00:00:00pages
191-205issue
1eissn
1755-098Xissn
1755-0998journal_volume
19pub_type
杂志文章abstract::Improving the realism of spatially explicit demographic models is important for better inferring the history of past populations and for understanding the genetic bases of adaptation and speciation. One particular type of demographic event to take into account is long-distance dispersal (LDD). The goals of this study ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2010.02881.x
更新日期:2010-09-01 00:00:00
abstract::Entomopathogenic fungi in the genus Metarhizium are useful for biological control programmes against economically important arthropod pests worldwide. However, understanding the true diversity and ecology of these organisms is hampered by convergent morphologies between species. The application of molecular techniques...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12058
更新日期:2013-03-01 00:00:00
abstract::Two of the five subspecies of the western big-eared bat, Corynorhinus townsendii, are listed as federally endangered with the remaining three being of conservation concern. Knowing the degree of connectivity among populations would aid in the establishment of sound conservation and management plans for this taxon. For...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02243.x
更新日期:2009-01-01 00:00:00
abstract::Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling improves, we ignore LD at our peril. If we sample variation at 10 loci in an organism with 20 chromosomes, we can reasonably treat them as 10 'independe...
journal_title:Molecular ecology resources
pub_type: 新闻
doi:10.1111/1755-0998.12424
更新日期:2015-09-01 00:00:00
abstract::Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing error...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12343
更新日期:2015-07-01 00:00:00
abstract::Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenc...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13160
更新日期:2020-07-01 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::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::Eleven microsatellites were characterized for Semicossyphus pulcher (California sheephead) using an enrichment protocol. The number of alleles varied from three to 14 for a sample of 40 individuals from two populations. Expected heterozygosities ranged from 0.311 to 0.891. All loci but one were in Hardy-Weinberg equil...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02467.x
更新日期:2009-01-01 00:00:00
abstract::The 'Symphyta' is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5360 specimens of 'Symphyta', m...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12614
更新日期:2017-07-01 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::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::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::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
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03141.x
更新日期:2012-07-01 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::A genomic library was constructed and 13 polymorphic microsatellite markers were developed for Hakea oldfieldii, a woody shrub endemic to southwest Western Australia. Polymorphism was investigated for these markers in 28 individuals from a single population located in restricted habitat at the base of the Whicher Rang...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02616.x
更新日期:2009-07-01 00:00:00
abstract::We developed 11 polymorphic microsatellite DNA markers for an Australian native plant, Daviesia triflora. The number of alleles per locus in 40 individuals varied from four to 19, and observed and expected heterozygosities ranged from 0.450 to 0.925 and from 0.497 to 0.899, respectively. Nine loci showed no significan...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02286.x
更新日期:2008-11-01 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::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::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::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::This article documents the public availability of raw transcriptome sequence data and 63,020 SNPs for the polar bear (Ursus maritimus). ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12190
更新日期:2014-01-01 00:00:00
abstract::Molecular genetic estimates of population effective size (Ne ) lose accuracy and precision when insufficient numbers of samples or loci are used. Ideally, researchers would like to forecast the necessary power when planning their project. neogen (genetic Ne for Overlapping Generations) enables estimates of precision a...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12941
更新日期:2019-01-01 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::Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used fo...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02699.x
更新日期:2009-09-01 00:00:00
abstract::Genomic data sets are increasingly central to ecological and evolutionary biology, but far fewer resources are available for invertebrates. Powerful new computational tools and the rapidly decreasing cost of Illumina sequencing are beginning to change this, enabling rapid genome assembly and reference marker extractio...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13146
更新日期:2020-05-01 00:00:00
abstract::Stegodyphus lineatus spiders live in groups consisting of closely related individuals. There appears to be no discrimination against related individuals as mates but females mate multiply, despite the fact that matings are shown to carry a cost. We have developed eight polymorphic dinucleotide microsatellite markers t...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02296.x
更新日期:2009-01-01 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
pub_type: 杂志文章,评审
doi:10.1111/1755-0998.12959
更新日期:2019-01-01 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
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03170.x
更新日期:2012-11-01 00:00:00
abstract::Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus and Leucocytoozoon) represent an exciting multihost, multiparasite system in ecology and evolution. Global research in this field accelerated after the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barco...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12977
更新日期:2019-03-01 00:00:00