Preprints (not yet peer-reviewed)

58 downloads
89 views

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data...

["Biodiversity","Bioinformatics","Computational Biology","Microbiology"]
doi:10.7287/peerj.preprints.2941v1
85 downloads
309 views

The use of online data repositories and the establishment of new data standards that require data to be computer-parsable so that algorithms can reason over them have become increasingly important with the emergence of high-throughput technologies, Big Data and...

["Biodiversity","Bioinformatics","Computational Biology","Zoology","Computational Science"]
doi:10.7287/peerj.preprints.2429v2
307 downloads
962 views

The dynamics of ecological communities have been described by neutral and niche theories that are now increasingly integrated into unified models. It is known that a critical transition exists between these two states, but the spatial aspect of this transition...

["Biodiversity","Computational Biology","Ecology","Mathematical Biology"]
doi:10.7287/peerj.preprints.1589v4
39 downloads
183 views

The scientific literature contains an historic record of the changing ways in which we describe the world. Shifts in understanding of scientific concepts are reflected in the introduction of new terms and the changing usage and context of existing ones. We conducted...

["Biodiversity","Bioinformatics","Computational Biology","Computational Science"]
doi:10.7287/peerj.preprints.2747v1
308 downloads
2,567 views

Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing metagenomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar 2010) for which the source code is not publicly available,...

["Biodiversity","Bioinformatics","Computational Biology","Genomics","Microbiology"]
doi:10.7287/peerj.preprints.2409v1
152 downloads
344 views

Predicting potential distribution for alien plants by species distribution model (SDM, or Ecological Niche Model) using occurrence data and habitat environmental variables plays an important role in management of the invasive risk by an alien plant. Common groundsels...

["Biodiversity","Biogeography","Computational Biology","Ecology","Plant Science"]
doi:10.7287/peerj.preprints.1612v1
121 downloads
245 views

The growing number of wildlife endocrinology studies have greatly enhanced our understanding of comparative endocrinology, and have also generated extensive longitudinal data for a vast number of species. However, the extensive graphical analysis required for these...

["Biodiversity","Computational Biology","Diabetes and Endocrinology"]
doi:10.7287/peerj.preprints.1546v1
206 downloads
383 views

Anchors are important attachment appendages that prevent the physical dislodging of a monogenean parasite from fish host gills. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation...

["Biodiversity","Computational Biology","Evolutionary Studies","Taxonomy","Zoology"]
doi:10.7287/peerj.preprints.1283v1
73 downloads
173 views

The concept of phylogenetic homology has been criticized of involving circular argumentation resulting from a methodological gap between its ontological definition and its empirical recognition criteria. Based on the role of similarity for the recognition of phylogenetic...

["Biodiversity","Bioinformatics","Computational Biology","Evolutionary Studies","Zoology"]
doi:10.7287/peerj.preprints.1243v1
281 downloads
360 views

The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities...

["Biodiversity","Computational Biology","Ecology","Plant Science"]
doi:10.7287/peerj.preprints.927v1
182 downloads
547 views

The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in non-computer readable...

["Biodiversity","Bioinformatics","Computational Biology","Evolutionary Studies"]
doi:10.7287/peerj.preprints.807v1
175 downloads
594 views

Background: Mexico is the fourth richest country in amphibians and the second country with the highest quantity of threatened amphibian species, and this number could be higher as many species are too poorly known to be accurately assigned to a risk category. The...

["Biodiversity","Bioinformatics","Computational Biology","Conservation Biology"]
doi:10.7287/peerj.preprints.490v2
319 downloads
1,233 views

Ecological variables such as species richness (S) and total abundance (N) can strongly influence ecological patterns. For example, the general form of the species abundance distribution (SAD) can often be explained by the majority of possible forms having the same...

["Biodiversity","Computational Biology","Ecology","Mathematical Biology","Computational Science"]
doi:10.7287/peerj.preprints.78v2
166 downloads
465 views

The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees; the methods are illustrated using honeybee viral samples. The paper has two findings. First, a method for correction of next generation sequencing error...

["Biodiversity","Bioinformatics","Computational Biology","Genetics","Mathematical Biology"]
doi:10.7287/peerj.preprints.441v1
742 downloads
938 views

The structure pattern of the tree of life clues on the key ecological issues; hence knowing the fractal dimension is the fundamental question in understanding the tree of life. Yet the fractal dimension of the tree of life remains unclear since the scale of the...

["Biodiversity","Computational Biology","Ecology","Evolutionary Studies","Taxonomy"]
doi:10.7287/peerj.preprints.198v3
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