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81.
We describe polymerase chain reaction primers that amplify the low-copy nuclear adenine nucleotide transporter gene in decapod crustaceans. These were tested on 35 species from 14 decapod families, and a single polymerase chain reaction product amplified in 32 species. Of 49 sequences generated, only two did not contain an intron, and the longest intron identified was more than 834 nucleotides in length. The amplified fragment is likely to be useful at various taxonomic levels. While the intron is suitable for phylogeographical/population genetic studies and to identify cryptic speciation, the second exon region is sufficiently long to provide signal at both the phylogeographical and phylogenetic levels. 相似文献
82.
We critically compared Marcusenius specimens from the mouth of the Cunene River on the Namibia/Angola border, a harsh desert environment on the Atlantic Ocean coast virtually devoid of aerial insects with aquatic larvae which are an important food item, with Marcusenius multisquamatus Kramer & Wink, 2013 from the escarpment region of that same river, in a relatively rich and productive subtropical savannah environment. River mouth specimens were differentiated in morphology and electric organ discharges, as determined by ANOVA/MANOVA comparisons, principal component and discriminant analyses on morphological and electrophysiological characters, and genetics, including sequences of the mitochondrial cytochrome b gene, indicating reproductive isolation. Specimens from the river mouth differed from M. multisquamatus, their closest relatives, by having a shorter snout, a smaller eye diameter, and smaller nares separation. River mouth specimens were also differentiated from other, increasingly less-close relatives, such as M. altisambesi Kramer et al., 2007 from the Okavango River, Botswana, and from M. krameri Maake et al., 2014 from the Limpopo System, South Africa. We therefore designate the new species Marcusenius desertus sp. nov. for the Cunene River mouth population. 相似文献
83.
Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully assessed when planning population genetic studies of cetaceans. 相似文献
84.
M. C. Arias Christiane Atteke S. C. Augusto J. Bailey Pilar Bazaga Luciano B. Beheregaray Laure Benoit Rumsaïs Blatrix Céline Born R. M. Brito Hai‐kui Chen Sara Covarrubias Clara de Vega Champlain Djiéto‐Lordon Marie‐Pierre Dubois F. O. Francisco Cristina García P. H. P. Gonçalves Clementina González Carla Gutiérrez‐Rodríguez Michael P. Hammer Carlos M. Herrera H. Itoh S. Kamimura H. Karaoglu S. Kojima Shou‐Li Li Hannah J. Ling Pável F. Matos‐Maraví Doyle McKey Judicaël Mezui‐M'Eko Juan Francisco Ornelas R. F. Park María I. Pozo Satu Ramula Cristina Rigueiro Jonathan Sandoval‐Castillo L. R. Santiago Miyuki M. Seino Chang‐Bing Song H. Takeshima Anti Vasemägi C. R. Wellings Ji Yan Du Yu‐Zhou Chang‐Rong Zhang Tian‐Yun Zhang 《Molecular ecology resources》2013,13(4):760-762
This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross‐tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii. 相似文献
85.
Gregoire Masliah Christophe Maris Sebastian LB König Maxim Yulikov Florian Aeschimann Anna L Malinowska Julie Mabille Jan Weiler Andrea Holla Juerg Hunziker Nicole Meisner‐Kober Benjamin Schuler Gunnar Jeschke Frederic H‐T Allain 《The EMBO journal》2018,37(6)
The accurate cleavage of pre‐micro(mi)RNAs by Dicer and mi/siRNA guide strand selection are important steps in forming the RNA‐induced silencing complex (RISC). The role of Dicer binding partner TRBP in these processes remains poorly understood. Here, we solved the solution structure of the two N‐terminal dsRNA binding domains (dsRBDs) of TRBP in complex with a functionally asymmetric siRNA using NMR, EPR, and single‐molecule spectroscopy. We find that siRNA recognition by the dsRBDs is not sequence‐specific but rather depends on the RNA shape. The two dsRBDs can swap their binding sites, giving rise to two equally populated, pseudo‐symmetrical complexes, showing that TRBP is not a primary sensor of siRNA asymmetry. Using our structure to model a Dicer‐TRBP‐siRNA ternary complex, we show that TRBP's dsRBDs and Dicer's RNase III domains bind a canonical 19 base pair siRNA on opposite sides, supporting a mechanism whereby TRBP influences Dicer‐mediated cleavage accuracy by binding the dsRNA region of the pre‐miRNA during Dicer cleavage. 相似文献
86.
Rogers AR; Fraley AE; Bamshad MJ; Watkins WS; Jorde LB 《Molecular biology and evolution》1996,13(7):895-902
Mismatch distributions are histograms showing the pattern of nucleotide (or
restriction) site differences between pairs of individuals in a sample.
They can be used to test hypotheses about the history of population size
and subdivision (if selective neutrality is assumed) or about selection (if
a constant population size is assumed). Previous work has assumed that
mutations never strike the same site twice, an assumption that is called
the model of infinite sites. Fortunately, the results are surprisingly
robust even when this assumption is violated. We show here that (1)
confidence regions inferred using the infinite- sites model differ little
from those inferred using a model of finite sites with uniform
site-specific mutation rates, and (2) even when site- specific mutation
rates follow a gamma distribution, confidence regions are little changed
until the gamma shape parameter falls well below its plausible range, to
roughly 0.01. In addition, we evaluate and reject the proposition that
mismatch waves are produced by pooling data from several subdivisions of a
structured population.
相似文献
87.
Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc,the greenlip abalone (Haliotis laevigata), along a longitudinal environmental gradient 下载免费PDF全文
Jonathan Sandoval‐Castillo Nick A. Robinson Anthony M. Hart Lachlan W. S. Strain Luciano B. Beheregaray 《Molecular ecology》2018,27(7):1603-1620
Populations of broadcast spawning marine organisms often have large sizes and are exposed to reduced genetic drift. Under such scenarios, strong selection associated with spatial environmental heterogeneity is expected to drive localized adaptive divergence, even in the face of connectivity. We tested this hypothesis using a seascape genomics approach in the commercially important greenlip abalone (Haliotis laevigata). We assessed how its population structure has been influenced by environmental heterogeneity along a zonal coastal boundary in southern Australia linked by strong oceanographic connectivity. Our data sets include 9,109 filtered SNPs for 371 abalones from 13 localities and environmental mapping across ~800 km. Genotype–environment association analyses and outlier tests defined 8,786 putatively neutral and 323 candidate adaptive loci. From a neutral perspective, the species is better represented by a metapopulation with very low differentiation (global FST = 0.0081) and weak isolation by distance following a stepping‐stone model. For the candidate adaptive loci, however, model‐based and model‐free approaches indicated five divergent population clusters. After controlling for spatial distance, the distribution of putatively adaptive variation was strongly correlated to selection linked to minimum sea surface temperature and oxygen concentration. Around 80 candidates were annotated to genes with functions related to high temperature and/or low oxygen tolerance, including genes that influence the resilience of abalone species found in other biogeographic regions. Our study includes a documented example about the uptake of genomic information in fisheries management and supports the hypothesis of adaptive divergence due to coastal environmental heterogeneity in a connected metapopulation of a broadcast spawner. 相似文献
88.
Leanne K. Faulks Dean M. Gilligan Luciano B. Beheregaray 《Journal of Biogeography》2010,37(7):1329-1340
Aim We conducted a range‐wide phylogeographic study of a common Australian freshwater fish, the golden perch (Macquaria ambigua), to investigate the relationship between environmental processes and evolutionary history in drainage basins. Location Inland [Lake Eyre (LEB), Murray–Darling (MDB) and Bulloo (BULL)] and coastal basins [Fitzroy (FITZ)] of eastern Australia. Methods A total of 590 samples were collected from across the entire species’ distribution and a section of the mitochondrial DNA control region was sequenced. In order to reconstruct the evolutionary history of M. ambigua a comprehensive suite of phylogeographic analyses was conducted, including nested clade phylogeographic analysis, mismatch analysis and isolation‐with‐migration model simulations. Results Three major lineages corresponding to the major drainage basins, FITZ, MDB and LEB/BULL, were identified (ΦST = 0.92). Lineages from the coastal basin (FITZ) were highly divergent from those of the inland basins (up to 6%). Levels of genetic diversity in the inland basins were relatively low and our analyses indicate that these populations experienced both demographic and range expansions during the Pleistocene. Main conclusions Investigation of the range‐wide phylogeography of M. ambigua has revealed new insights into the biogeography of the Australian arid zone, particularly with regard to evolutionary events chronologically associated with cyclical moist and dry conditions. We propose that M. ambigua originated on the east coast (FITZ) and crossed a major geographic barrier, the Great Dividing Range (GDR), to colonize the inland basins (MDB, LEB and BULL). We infer a series of demographic and range expansion events for M. ambigua consistent with a scenario of moister Pleistocene conditions and increased connectivity of freshwater environments, both within and among drainage basins. Major lineages then diversified following isolation of freshwater environments under increasingly arid climate conditions. We suggest that management priorities for M. ambigua should include the resolution of taxonomic uncertainties and the maintenance of genetic diversity of both stocked populations in the MDB and native populations of the LEB that may be at risk of further isolation and reduced gene flow due to increased aridification under future climate change scenarios. 相似文献
89.
90.
In anticipation of the publication of full revisions, a diagnosis of a new species of Droguetia is presented together with two new combinations for subspecies of Droguetia iners , a new combination for a species and a variety on Didymodoxa and a new combination for a subspecies of Australina pusilla . The name Elatostema trinerve Hochst. (1845) is shown to be conspecific with and antedate Urera cameroonensis Wedd. (1869). The new combination Urera trinervis is therefore made. 相似文献