Today, we’re pleased to announce that we’re launching a new article type for Methods in Ecology and Evolution: Practical Tools. Like our Applications articles, Practical Tools will be short papers(up to 3000 words). They’ll focus on new field techniques, equipment or lab protocols. From this point forward, our Applications papers will solely focus on software and code.
Practical tools need to clearly demonstrate how tools designed for specific systems or problems can be adapted for more general use. Online supporting information can include specific instructions, especially for building equipment. You can find some examples of Applications that would now fit into this article type here and here.
This double-sized issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.
–Phylogenetic Trees: The fields of phylogenetic tree and network inference have advanced independently, with only a few attempts to bridge them. Schliep et al. provide a framework, implemented in R, to transfer information between trees and networks.
–Emon: Studies, surveys and monitoring are often costly, so small investments in preliminary data collection and systematic planning of these activities can help to make best use of resources. To meet recognised needs for accessible tools to plan some aspects of studies, surveys and monitoring, Barry et al. developed the R package emon, which includes routines for study design through power analysis and feature detection.
–Haplostrips: A tool to visualise polymorphisms of a given region of the genome in the form of independently clustered and sorted haplotypes. Haplostrips is a command-line tool written in Python and R, that uses variant call format files as input and generates a heatmap view.
A new technique makes it possible to cost-effectively analyse genetic material from fossil plants and animals. Researchers from the Swiss Federal Institute for Forest, Snow and Landscape Research WSL and the universities of Lausanne and Bern have used this technique to examine the DNA of silver fir remains found in lake sediment in Ticino. They found clues as to how forests reacted to the emergence of agriculture.
The new process utilises the latest advances in DNA technology to isolate ancient DNA (aDNA) from prehistoric plants and animals. The techniques used to date are, however, expensive. “As population geneticists often need several dozens samples to make reliable statements, many research ideas are not currently financially viable,” says Nadir Alvarez, a professor at the University of Lausanne’s Department of Ecology and Evolution.
The research team led by Alvarez and his colleagues Christoph Sperisen (a population geneticist at the WSL), Willy Tinner (a professor of palaeoecology at the University of Bern) and Sarah Schmid (a biologist from the University of Lausanne) has now developed a cost-effective alternative and demonstrated its potential with subfossil silver fir needles found at Origlio lake in Ticino. The team showcased the results in the research journal Methods in Ecology and Evolution. Continue reading →