On top of the list, is “A consumer’s guide to nestedness analysis” by Werner Ulrich, Mário Almeida-Neto and Nicholas J. Gotelli.
Here is a short description by Werner Ulrich, on what it’s all about:
Ecologists look for patterns in nature. The nested pattern – in which the composition of small assemblages is a nested subset of larger ones – is one that received a lot of attention, both because it is so simple and because it is so common. In biogeography, if sites are ordered by area or along an environmental gradient, a nested pattern can be interpreted as an orderly loss of species along the gradient. This is the most common interpretation of nestedness. It was popularized in the 1980s by Bruce Patterson and the late Wirt Atmar, who introduced a nestedness temperature calculator, compiled a large set of ecological presence-absence matrices from the published literature, and detected nestedness in most of them. Since then, much research has been devoted to articulating alternative mechanisms for nestedness, and developing appropriate metrics and null models for testing the pattern. Nestedness has also been used in food web or species interaction analysis, population genetics, and even molecular biology. However, the nestedness tale is also a story of failure and a warning on the challenges of statistical pattern analysis in ecology. Many studies have unfortunately used ad hoc measures of the degree of nestedness, inappropriate statistical benchmarks, and questionable ecological arguments. That was the point where we (Nick, Mario, and I) stepped in. The origin of our “consumer’s guide” paper was from an idea of Mario’s, who noticed that the quantification of a nested pattern went into a wrong direction. He asked me to take part in the development of a new metric, and the resulting Oikos paper was a success. We then tried to give guidelines for proper pattern identification and testing. During the writing, we noticed how many snags even a simple pattern like the nested one provides for researchers. Apparently, many other scientists shared our views. Our impression is that the quality of nestedness research has improved during the last few years, and we hope that our review has contributed to that trend.
During the work on nestedness, we started developing new metrics to quantify observed patterns and expanded the framework for proper statistical testing. Two new Oikos papers by Nick and me on statistical challenges and on pattern detection in ecology are the fruits of these efforts. We can only hope they will become as popular as the “consumer’s guide” to nestedness.’