Related papers: The Dawn of Open Access to Phylogenetic Data
This study analyzes rates and ways of data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on human ancient DNA published between 1988 and 2013. For the most part, data are available in…
Policies ensuring that research data are available on public archives are increasingly being implemented at the government [1], funding agency [2-4], and journal [5,6] level. These policies are predicated on the idea that authors are poor…
Data sharing is fundamental to scientific progress, enhancing transparency, reproducibility, and innovation across disciplines. Despite its growing significance, the variability of data-sharing practices across research fields remains…
To improve the quality and efficiency of research, groups within the scientific community seek to exploit the value of data sharing. Funders, institutions, and specialist organizations are developing and implementing strategies to encourage…
With the rise of Wikipedia as a first-stop source for scientific knowledge, it is important to compare its representation of that knowledge to that of the academic literature. Here we identify the 250 most heavily used journals in each of…
In recent years, funding agencies and journals increasingly advocate for open science practices (e.g. data and method sharing) to improve the transparency, access, and reproducibility of science. However, quantifying these practices at…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of…
Data sharing by researchers is a centerpiece of Open Science principles and scientific progress. For a sample of 6019 researchers, we analyze the extent/frequency of their data sharing. Specifically, the relationship with the following four…
Scholarly publishing involves multiple stakeholders having various types of interest. In Canada, the implication of universities, the presence of societies and the availability of governmental support for periodicals seem to have…
The phylogenetic network emerged in the 1990s as a new model to represent the evolution of species in the case where coexisting species transfer genetic information through hybridization, recombination, lateral gene transfer, etc. As is…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Without sufficient information about research data practices occurring in a particular research organisation, there is a risk of mismatching research data service efforts with the needs of its researchers. This study describes how data…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…