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251.
Alex R. Van Dam Javier O. Covas Orizondo Athena W. Lam Duane D. McKenna Matthew H. Van Dam 《Ecology and evolution》2022,12(3)
Phylogenomics via ultraconserved elements (UCEs) has led to improved phylogenetic reconstructions across the tree of life. However, inadvertently incorporating non‐targeted DNA into the UCE marker design will lead to misinformation being incorporated into subsequent analyses. To date, the effectiveness of basic metagenomic filtering strategies has not been assessed in arthropods. Designing markers from museum specimens requires careful consideration of methods due to the high levels of microbial contamination typically found in such specimens. We investigate if contaminant sequences are carried forward into a UCE marker set we developed from insect museum specimens using a standard bioinformatics pipeline. We find that the methods currently employed by most researchers do not exclude contamination from the final set of targets. Lastly, we highlight several paths forward for reducing contamination in UCE marker design. 相似文献
252.
High‐elevation organisms are expected to evolve physiological adaptations to cope with harsh environmental conditions. Yet, evidence for such adaptive differences, especially compared to closely related lowland taxa occurring along the same elevational gradient, is rare. Revisiting an anecdotal natural history observation by O. Bangs from 1899 and based on new measurements of museum specimens, we confirmed that the high‐elevation hermit wood wren (Henicorhina anachoreta) from the Sierra Nevada de Santa Marta, Colombia, has longer, more insulative feathers on the chest and back, than its lower‐elevation counterpart the grey‐breasted wood wren (H. leucophrys). However, we did not find evidence for the same specializations in subspecies of H. leucophrys that live at high elevations on other elevational gradients in the Colombian Andes, although similar adaptive solutions have arisen in separate mountain systems like the Himalayas. Adaptations in plumage may be associated with the recurrence of elevational species replacements throughout the tropics. 相似文献
253.
Early evolutionary history of the flowering plant family Annonaceae: steady diversification and boreotropical geodispersal 总被引:1,自引:0,他引:1
Thomas L. P. Couvreur Michael D. Pirie Lars W. Chatrou Richard M. K. Saunders Yvonne C. F. Su James E. Richardson Roy H. J. Erkens 《Journal of Biogeography》2011,38(4):664-680
Aim Rain forest‐restricted plant families show disjunct distributions between the three major tropical regions: South America, Africa and Asia. Explaining these disjunctions has become an important challenge in biogeography. The pantropical plant family Annonaceae is used to test hypotheses that might explain diversification and distribution patterns in tropical biota: the museum hypothesis (low extinction leading to steady accumulation of species); and dispersal between Africa and Asia via Indian rafting versus boreotropical geodispersal. Location Tropics and boreotropics. Methods Molecular age estimates were calculated using a Bayesian approach based on 83% generic sampling representing all major lineages within the family, seven chloroplast markers and two fossil calibrations. An analysis of diversification was carried out, which included lineage‐through‐time (LTT) plots and the calculation of diversification rates for genera and major clades. Ancestral areas were reconstructed using a maximum likelihood approach that implements the dispersal–extinction–cladogenesis model. Results The LTT plots indicated a constant overall rate of diversification with low extinction rates for the family during the first 80 Ma of its existence. The highest diversification rates were inferred for several young genera such as Desmopsis, Uvariopsis and Unonopsis. A boreotropical migration route was supported over Indian rafting as the best fitting hypothesis to explain present‐day distribution patterns within the family. Main conclusions Early diversification within Annonaceae fits the hypothesis of a museum model of tropical diversification, with an overall steady increase in lineages possibly due to low extinction rates. The present‐day distribution of species within the two largest clades of Annonaceae is the result of two contrasting biogeographic histories. The ‘long‐branch clade’ has been diversifying since the beginning of the Cenozoic and underwent numerous geodispersals via the boreotropics and several more recent long‐distance dispersal events. In contrast, the ‘short‐branch clade’ dispersed once into Asia via the boreotropics during the Early Miocene and further dispersal was limited. 相似文献
254.
Avian eggshell is a bio‐ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historical populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more‐diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40–60‐year‐old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterize the yield and quality of such DNA. In doing so, we describe the first protocol for successful extraction of intracrystalline DNA from neognath eggshells, with the view to unlocking the potential of vast museum egg collections for genetic research. We were able to retrieve DNA fragments over 200 bp in length from 10 mg of eggshell powder from all three specimens, and demonstrate that expanding the existing blow‐hole can allow sufficient material to be collected for DNA extraction while minimizing damage to the appearance and structural integrity of the egg. Furthermore, we were able to reconstruct near‐complete mitochondrial genomes at a coverage of 40‐83X through shotgun sequencing of these extracts on three NextSeq lanes. Given the current extinction and extirpation rates of many avian species world‐wide, genetic data from eggshell could provide a rapid and cost‐effective approach to examining temporal changes in avian diversity, which is not only becoming crucial for conservation management, but also serve to deepen our understanding of genome‐wide evolutionary processes. 相似文献
255.
Estimates of the number of mounted pteridophyte specimens in six major herbaria in the United States
Robbin C. Moran 《Brittonia》2001,53(3):435-436
A stratified-random sampling method was used to estimate the number of pteridophyte specimens in six of the largest herbaria
in the United states (F, GH/A/NEBC, MO, NY, UC, US). The point estimate of the collection size and the 95% confidence intervals
for each herbarium were found to be as follows: US 251,000 (±20,000); NY 201,000 (±20,000); MO 160,000 (±15,000); GH/A/NEBC
124,000 (±12,000); UC 119,000 (±9,000); F 97,000 (±10,000). It is hoped that these numbers will help assess the growth of
these collections in the future. 相似文献
256.
Johnson et al. (2013) found that morphometric measurements of dragonfly wings taken from actual specimens and measurements taken from whole-drawer images of those specimens were equally accurate. We do not believe that their conclusions are justified by their data and analysis. Our reasons are, first, that their study was constrained in ways that restrict the generalisability of their results, but second, and of far greater significance, their statistical approach was entirely unsuited to their data and their results misled them to erroneous conclusions. We offer an alternative analysis of their data as published. Our reanalysis demonstrates, contra Johnson et al., that measurements from scanned images are not a reliable substitute for direct measurement. 相似文献
257.
A protocol used routinely for rapid ancient DNA extraction was applied to fish tissue archived over 80 years ago. The method proved successful, whereas other extraction protocols failed. Researchers working on DNA from older archived fish samples are encouraged to continue to concentrate their efforts on 'white-eye' specimens, which indicate an alcohol-based fixative and are thus likely to yield viable DNA. 相似文献
258.
Digitarium is a joint initiative of the Finnish Museum of Natural History and the University of Eastern Finland. It was established in 2010 as a dedicated shop for the large-scale digitisation of natural history collections. Digitarium offers service packages based on the digitisation process, including tagging, imaging, data entry, georeferencing, filtering, and validation. During the process, all specimens are imaged, and distance workers take care of the data entry from the images. The customer receives the data in Darwin Core Archive format, as well as images of the specimens and their labels. Digitarium also offers the option of publishing images through Morphbank, sharing data through GBIF, and archiving data for long-term storage. Service packages can also be designed on demand to respond to the specific needs of the customer. The paper also discusses logistics, costs, and intellectual property rights (IPR) issues related to the work that Digitarium undertakes. 相似文献
259.
260.
Harvestmen of the BOS Arthropod Collection of the University of Oviedo (Spain) (Arachnida,Opiliones)
There are significant gaps in accessible knowledge about the distribution and phenology of Iberian harvestmen (Arachnida: Opiliones). Harvestmen accessible datasets in Iberian Peninsula are unknown, an only two other datasets available in GBIF are composed exclusively of harvestmen records. Moreover, only a few harvestmen data from Iberian Peninsula are available in GBIF network (or in any network that allows public retrieval or use these data). This paper describes the data associated with the Opiliones kept in the BOS Arthropod Collection of the University of Oviedo, Spain (hosted in the Department of Biología de Organismos y Sistemas), filling some of those gaps. The specimens were mainly collected from the northern third of the Iberian Peninsula. The earliest specimen deposited in the collection, dating back to the early 20th century, belongs to the P. Franganillo Collection. The dataset documents the collection of 16,455 specimens, preserved in 3,772 vials. Approximately 38% of the specimens belong to the family Sclerosomatidae, and 26% to Phalangidae; six other families with fewer specimens are also included. Data quality control was incorporated at several steps of digitisation process to facilitate reuse and improve accuracy. The complete dataset is also provided in Darwin Core Archive format, allowing public retrieval, use and combination with other biological, biodiversity of geographical variables datasets. 相似文献