nestedness
Nestedness is a measure of structure in an ecological system, usually applied to species-sites systems (describing the distribution of species across locations), or species-species interaction networks (describing the interactions between species, usually as bipartite networks such as hosts-parasites, plants-pollinators, etc.).
A system (usually represented as a matrix) is said to be nested when the elements that have a few items in them (locations with few species, species with few interactions) have a subset of the items of elements with more items. Imagine a series of islands that are ordered by their distance from the mainland. If the mainland has all species, the first island has a subset of mainland's species, the second island has a subset of the first island's species, and so forth, then this system is perfectly nested.
Measures of nestedness
One measurement unit for nestedness is a system's 'temperature' offered by Atmar and Patterson in 1993.{{cite journal |author=Patterson and Atmar |year=1993 |title=The measure of order and disorder in the distribution of species in fragmented habitat |journal=Oecologia |volume=96 |pages=373–382 |doi=10.1007/BF00317508 |pmid=28313653 |last2=Patterson |first2=Bruce D. |issue=3|bibcode=1993Oecol..96..373A |s2cid=12177277 }} This measures the order in which species' extinctions would occur in the system (or from the other side - the order of colonizing a system). The 'colder' the system is, the more fixed the order of extinction would be. In a warmer system, extinctions will take a more random order. Temperatures go from 0°, coldest and absolutely fixed, to 100° absolutely random.
For various reasons, the Nestedness Temperature Calculator is not mathematically satisfying (no unique solution, not conservative enough).{{cite journal|vauthors=Rodríguez-Gironés MA, Santamaría L |year=2006 |title=A new algorithm to calculate the nestedness temperature of presence–absence matrices |journal=Journal of Biogeography |volume=33|pages=924–935 |doi=10.1111/j.1365-2699.2006.01444.x|issue=5|s2cid=84989243 }}{{cite journal|author=Guimarães, P. R., P. Guimarães |year=2006 |title=Improving the analyses of nestedness for large sets of matrices |journal=Environmental Modelling and Software |volume=21|pages=1512–1513 |doi=10.1016/j.envsoft.2006.04.002|issue=10}} A software (BINMATNEST) is available from the authors on request and from the Journal of Biogeography to correct these deficits {{Cite journal | doi=10.1111/j.1365-2699.2006.01444.x| title=A new algorithm to calculate the nestedness temperature of presence-absence matrices| journal=Journal of Biogeography| volume=33| issue=5| pages=924–935| year=2006| last1=Rodriguez-Girones| first1=Miguel A.| last2=Santamaria| first2=Luis| s2cid=84989243}} In addition, ANINHADO solves problems of large matrix size and processing of a large number of randomized matrices; in addition it implements several null models to estimate the significance of nestedness.{{cite journal | doi = 10.1016/j.envsoft.2006.04.002 | volume=21 | issue=10 | title=Improving the analyses of nestedness for large sets of matrices | journal=Environmental Modelling | pages=1512–1513| year=2006 | last1=Guimaraesjr | first1=P. | last2=Guimaraes | first2=P. }}http://www.iemss.org/shortcom/software/software.php?aid=201{{Dead link|date=October 2019 |bot=InternetArchiveBot |fix-attempted=yes }}
Bastolla et al. introduced a simple measure of nestedness based on the number of common neighbours for each pair of nodes.{{cite journal|vauthors=Bastolla U, Fortuna MA, Pascual-García A, Ferrera A, Luque B, Bascompte J |year=2009 |title=The architecture of mutualistic networks minimizes competition and increases biodiversity |journal=Nature |volume=458 |issue=7241 |pages=1018–1020 |doi=10.1038/nature07950 |pmid=19396144|bibcode=2009Natur.458.1018B |s2cid=4395634 }} They argue that this can help reduce the effective competition between nodes in certain situations. For instance, two insect species might "help" each other by pollinating the same subset of plants, thereby reducing the extent to which they are harmful to each other. The authors suggest that this effect is behind a correlation between nestedness and diversity in plant-pollinator ecosystems. However, Johnson et al. have shown that this measure does not, in fact, properly account for the desired effect.{{cite journal|vauthors=Johnson S, Domínguez-García V, Muñoz MA |year=2013 |title=Factors Determining Nestedness in Complex Networks |journal=PLOS ONE |volume=8 |issue=9 |pages=e74025 |doi=10.1371/journal.pone.0074025|pmid=24069264 |pmc=3777946 |arxiv=1307.4685 |bibcode=2013PLoSO...874025J |doi-access=free }} These authors propose a refined version of the measure, and go on to show how certain network properties affect nestedness.
References
{{reflist}}
Software
- [https://web.archive.org/web/20061102085631/http://aics-research.com/nestedness/tempcalc.html Nestedness Temperature Calculator Program]
- [http://www.umk.pl/~ulrichw/Downloads.html#progr9 an Fortran Version correcting some of the initial problems, by Werner Ulrich, Poland]{{Dead link|date=October 2019 |bot=InternetArchiveBot |fix-attempted=yes }}
- [http://www.guimaraes.bio.br/sof.html ANINHADO, a Nestedness Temperature Calculator Program improving NTC for large matrices and implementing additional null models, by Paulo Guimarães and Paulo R. Guimarães Jr., Brazil]
- [http://hypatia.agricolas.upm.es/WINE/ Weighted Interaction Nestedness Estimator. It works with weighted matrices (i.e. species abundance)]
- [http://purl.oclc.org/ned NeD - Nestedness for Dummies. A user friendly interface for nestedness analysis]