a2b

Analysis of bipartite ecological networks

Version 1.0 - May 2015

The a2b computer program is designed to study bipartite ecological networks. Its merits are:

• Very easy to use
• Very efficient in terms of computation time
• Large panel of network descriptors
• Large database of bipartite ecological networks

The a2b program is distributed free of charge. Users are under their own responsibility.

 After installation, the a2b directory should contain:

• The a2b program executable file a2b.exe
• Text files *.ab0, *.ab1, *.ab2, *.ab3 describing example bipartite networks
• The reference manual a2bref.pdf

How to run the a2b program?

• Double-click on any file *.ab0. Select program a2b.exe to open the file
• The a2b program will then create the network described by the file and compute its descriptors
• Several commands allow to study the network
• For detailed informations consult a2bref.pdf

What is a bipartite ecological network?

In a bipartite network, 2 sets of nodes, here called A-species and B-species, are joined by interaction links. For example, in a plant-pollinator network, pollinators are the A-species, plants are the B-species, and links represent mutualistic interactions between plants and pollinators (feeding of pollinators on plants, plant gametes dispersal by pollinators). Other examples of bipartite ecological networks are host-parasite antagonistic networks, site-species biogeographical networks, plant-seed disperser mutualistic networks, male-female mating networks.
A bipartite network comprising A-species in number A and B-species in number B, is represented by a (0,1)-matrix M = (m_ab) that is rectangular of size AxB. The entry m_ab = 1/0 of the matrix M indicates the presence/absence of an interaction link between the A-species a and the B-species b. A matrix W = (w_ab) ascribing nonnegative weights w_ab to interaction links can also be introduced (A and W have the same nonzero entries). The matrix of weights represents biological values associated with  interactions, e.g., number of visits of plants by pollinators.

What is provided by the a2b program?

With the a2b program, several bipartite networks can be studied simultaneously, empirical ones, specified in text files, or synthetic (random) ones, created using predefined models. The networks can be edited and displayed graphically. Results are stored in text and graphic files.

Network descriptors proposed by a2b program allow to analyze patterns and functionalities of a given ecological network via its topological properties, in particular

• Modularity – existence of partially autonomous subsets of A-species and B-species,
• Nestedness - specialist species tend to be a subset of generalist species,
• Robustness – resilience of the network to species extinction.

These 3 notions are crucial for the functionality of the network. They are related in non obvious ways.

References

Atmar W & BD Patterson. 1993. The measure of order and disorder in the distribution of species in fragmented habitat. Oecologia 96:373–382.

Brualdi RA & JG Sanderson. 1999. Nested species subsets, gaps, and discrepancy. Oecologia 119:256–264.

Brualdi RA. 2006. Algorithms for constructing (0,1)-matrices with prescribed row and column sum vectors. Discrete Mathematics 306:3054–3062.

Memmott J, NM Waser & MV Price. 2004. Tolerance of pollination networks to species extinctions. Proceedings of the Royal Society B 271:2605–2611.

Olesen JM, J Bascompte, YL Dupont & P Jordano. 2007. The modularity of pollination networks. Proceedings of the National Academy of Sciences USA 104:19891–19896.

Staniczenko PPA, JC Kopp & S Allesina. 2013. The ghost of nestedness in ecological networks. Nature Communications 4, 1391, doi:10.1038/ncomms2422.

Thébault E. 2013. Identifying compartments in presence–absence matrices and bipartite networks: insights into modularity measures. Journal of Biogeography 40:759–768.

Thébault E & C Fontaine. 2010. Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329:853–856.

Author

Mail to Stéphane Legendre

Contribution

Elisa Thébault, Colin Fontaine.