Abstract:
:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For nonmodel organisms with adaptive key innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has been primarily used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genomewide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Kratochwil CF,Meyer Adoi
10.1111/1755-0998.12350subject
Has Abstractpub_date
2015-07-01 00:00:00pages
761-71issue
4eissn
1755-098Xissn
1755-0998journal_volume
15pub_type
杂志文章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::Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12562
更新日期:2017-05-01 00:00:00
abstract::DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located ins...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13212
更新日期:2020-11-01 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::Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next-generation sequenc...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12188
更新日期:2014-03-01 00:00:00
abstract::The public availability of large quantities of gene sequence data provides a valuable resource of the mining of Simple Sequence Repeat (SSR) molecular genetic markers for genetic analysis. These markers are inexpensive, require minimal labour to produce and can frequently be associated with functionally annotated gene...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12078
更新日期:2013-05-01 00:00:00
abstract::A variety of challenges arise when monitoring wildlife populations for disease. Sampling tissues can be invasive to hosts, and obtaining sufficient sample sizes can be expensive and time-consuming, particularly for rare species and when pathogen prevalence is low. Environmental DNA (eDNA)-based detection of pathogens ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12461
更新日期:2016-03-01 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::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::A novel set of microsatellite markers for mungbean [Vigna radiata (L.) Wilczek] was developed from the public sequence database. Seventy-eight primers were designed and evaluated for polymorphism among 22 cultivated accessions. Eight polymorphic loci detected two to three alleles per locus with an average of 2.25. The...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02655.x
更新日期:2009-05-01 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
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03057.x
更新日期:2012-01-01 00:00:00
abstract::We present the leaf and floral transcriptomes of two hybridizing bromeliad species that differ in their major pollinator systems. Here we identified candidate genes responsible for pollinator attraction and reproductive isolation in these two species. We searched for candidate genes involved in floral traits, such as ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12504
更新日期:2016-07-01 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::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
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2011.03002.x
更新日期:2011-07-01 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::Most hosts are concurrently or sequentially infected with multiple parasites; thus, fully understanding interactions between individual parasite species and their hosts depends on accurate characterization of the parasite community. For parasitic nematodes, noninvasive methods for obtaining quantitative, species-speci...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12382
更新日期:2015-09-01 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
pub_type: 杂志文章
doi:10.1111/1755-0998.12714
更新日期:2018-01-01 00:00:00
abstract::Studies on the biogeography of host-parasitoid interactions are scarce, mainly because of technical difficulties associated with rearing and species identification. DNA barcoding is increasingly recognized as a valuable tool for taxon identification, allowing to link different life history stages of a species. We eval...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2010.02889.x
更新日期:2011-01-01 00:00:00
abstract::Molecular markers have been used to identify the sex of sampled individuals for several decades, but the time-consuming development phase prevented their application in many systems. Recently, a growing number of papers have applied reduced-representation sequencing (RRS) protocols to the identification of sex-specifi...
journal_title:Molecular ecology resources
pub_type: 评论,新闻
doi:10.1111/1755-0998.12761
更新日期:2018-03-01 00:00:00
abstract::Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12594
更新日期:2017-05-01 00:00:00
abstract::Amplified fragment length polymorphism (AFLP) fingerprint data are now commonly collected using DNA sequencers. AFLP genotypes are still often scored by eye from such data - a time-consuming, error-prone and subjective process. We present a semi-automated method of genotyping sequencer-collected AFLPs at predefined fr...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2007.02073.x
更新日期:2008-07-01 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::To determine the visual sensitivities of an organism of interest, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is often used to quantify expression of the light-sensitive opsins in the retina. While qRT-PCR is an affordable, high-throughput method for measuring expression, it comes with inher...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13062
更新日期:2019-11-01 00:00:00
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 ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12653
更新日期:2017-11-01 00:00:00
abstract::Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss re...
journal_title:Molecular ecology resources
pub_type: 杂志文章,评审
doi:10.1111/1755-0998.12626
更新日期:2017-09-01 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::Introgression can be an important evolutionary force but it can also lead to species extinction and as such is a crucial issue for species conservation. However, introgression is difficult to detect, morphologically as well as genetically. Hybridization with domestic cats (Felis silvestris catus) is a major concern fo...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12075
更新日期:2013-05-01 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::Estimation of demographic history from nucleotide sequences represents an important component of many studies in molecular ecology. For example, knowledge of a population's history can allow us to test hypotheses about the impact of climatic and anthropogenic factors. In the past, demographic analysis was typically li...
journal_title:Molecular ecology resources
pub_type: 杂志文章,评审
doi:10.1111/j.1755-0998.2011.02988.x
更新日期:2011-05-01 00:00:00
abstract::Restriction-site-associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a f...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12206
更新日期:2014-05-01 00:00:00