ecological area-network relations: methodology Christopher Moore cs765: complex networks 16 November 2011

Transcription

1 ecological area-network relations: methodology Christopher Moore cs765: complex networks 16 November 2011

2

3 ecology: the study of the spatial and temporal patterns of the distribution and abundance of organisms, including causes and consequences (Scheiner and Willig 2008)

4 ecology: the study of the spatial and temporal patterns of the distribution and abundance of organisms, including causes and consequences (Scheiner and Willig 2008)

5 individuals species

6 individuals N-area relationship species

7 individuals N-area relationship species e.g., log N land verts. of Lake MI (Hatt 1948) (Preston 1962a, b) log area (sq. mi.)

8 individuals N-area relationship species s-area relationship e.g., log N land verts. of Lake MI (Hatt 1948) (Preston 1962a, b) log area (sq. mi.)

9 individuals N-area relationship species s-area relationship e.g., log N land verts. of Lake MI (Hatt 1948) (Preston 1962a, b) log area (sq. mi.) e.g., (Hubbell 2001)

10 main question: sub-questions:

11 main question: is there a relationship between area and community structure? sub-questions:

12 main question: is there a relationship between area and community structure? sub-questions: i. are antagonistic and mutualistic communities different in their structure? ii. how is the community structure different of an island and adjacent mainland?

13 hypothesis: community structure is strongly related to area size, with smaller and larger areas respectively subject to a higher degree of stochastic and biological processes

14 guide location (Googlemaps.com)

15 guide C.M. Gienger

16 taxa

17 guide taxa (nazflora.com) plants

18 guide taxa (nazflora.com) plants invertebrates

19 guide taxa birds (Pyramid Lake Paiute Tribe) invertebrates (nazflora.com) plants

20 guide taxa reptiles (prbase.com) birds (Pyramid Lake Paiute Tribe) invertebrates (nazflora.com) plants

21 guide taxa invertebrates reptiles mammals (UofMI.edu) (prbase.com) birds (Pyramid Lake Paiute Tribe) plants (nazflora.com)

22 types of data

23 types of data plants invertebrates reptiles birds mammals

24 plants invertebrates reptiles birds mammals types of data presence / absence p / a p / a p / a p / a p / a

25 types of data plants presence / absence p / a abundance invertebrates p / a relative reptiles p / a abundance birds p / a mammals p / a relative

26 types of data plants presence / absence p / a abundance other invertebrates p / a relative reptiles p / a abundance body size birds p / a mammals p / a relative body size

27 body size measurements snout to vent length snout to the tail base

28 metrics graphs networks Anaho mainland

29 metrics graphs networks Anaho mainland +, - +, + +, - +, + +, - antagonistic network (food web / trophic network) +, + mutualistic network

30 metrics graphs networks Anaho mainland +, - +, + +, - +, + unweighted unweighted unweighted unweighted weighted by: abundance body size weighted by: abundance body size +, - antagonistic network (food web / trophic network) +, + mutualistic network

31 metrics graphs networks Anaho mainland +, - +, + +, - +, + unweighted unweighted unweighted unweighted weighted by: abundance body size weighted by: abundance body size diversity diversity diversity diversity connectance connectance connectance connectance nestedness nestedness nestedness nestedness modularity modularity modularity modularity +, - antagonistic network (food web / trophic network) +, + mutualistic network

32 metrics diversity connectance nestedness modularity (Thébault and Fontaine 2010)

33 metrics diversity connectance nestedness modularity k (Thébault and Fontaine 2010)

34 metrics diversity connectance nestedness modularity k C = I / M (Thébault and Fontaine 2010)

35 metrics diversity connectance nestedness modularity k C = I / M (Thébault and Fontaine 2010)

36 metrics diversity connectance nestedness modularity k C = I / M (Bascompte and Jordano 2007 [figures]; Thébault and Fontaine 2010)

37 metrics diversity connectance nestedness modularity k C = I / M (Bascompte and Jordano 2007 [figures]; Thébault and Fontaine 2010)

38 metrics diversity connectance nestedness modularity k C = I / M (Thébault and Fontaine 2010)

39 guide FoodWeb3D El Verde rainforest Caribbean reef 1 UK grassland Caribbean reef 3 (Foodwebs.org;,Williams 2010,Yoon et al. 2004)

40

41 network metric area

42 network metric area

43 limitations making up edges (sound to a large degree) sampling efforts scale of area described

44 comments / questions?

45 literature cited Bascompte, J. and P. Jordano Plant-animal mutualistic networks: The architecture of biodiversity. Annual Review of Ecology Evolution and Systematics 38: Hubbell, S. P The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, New Jersey, U.S. Preston, F. W. 1962a. The canonical distribution of commonness and rarity: Part i. Ecology 43: Preston, F. W The canonical distribution of commonness and rarity: Part ii. Ecology 43: Scheiner, S. and M. Willig A general theory of ecology. Theoretical Ecology 1: Thébault, E. and C. Fontaine Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329: Williams, R. J Network3D Software. Microsoft Research, Cambridge, UK. Yoon, I., R.J. Williams, E. Levine, S. Yoon, J.A. Dunne, and N.D. Martinez Webs on the Web (WoW): 3D visualization of ecological networks on the WWW for collaborative research and education. Proceedings of the IS&T/SPIE Symposium on Electronic Imaging, Visualization and Data Analysis 5295:

46 nestedness Almeida-Neto, M., P. Guimarães, P. R. Guimarães, R. D. Loyola, and W. Ulrich A consistent metric for nestedness analysis in ecological systems: Reconciling concept and measurement. Oikos 117: other nestedness metrics

47 nestedness Almeida-Neto, M., P. Guimarães, P. R. Guimarães, R. D. Loyola, and W. Ulrich A consistent metric for nestedness analysis in ecological systems: Reconciling concept and measurement. Oikos 117: NDOF as a metric

48 nestedness Almeida-Neto, M., P. Guimarães, P. R. Guimarães, R. D. Loyola, and W. Ulrich A consistent metric for nestedness analysis in ecological systems: Reconciling concept and measurement. Oikos 117: comparison of NDOF to other metrics

49 nestedness Almeida-Neto, M., P. Guimarães, P. R. Guimarães, R. D. Loyola, and W. Ulrich A consistent metric for nestedness analysis in ecological systems: Reconciling concept and measurement. Oikos 117: trial run = SUCCESS!!! software ANINHADO ( nested in Portuguese) is a program developed for fast and autonomous calculation of two distinct measures of nestedness. Nestedness is a feature of binary matrices (also called presence/ absence matrices). The notion of nestedness is particularly relevant for studies focusing the patterns of species occurrence among a set of locations (e.g., islands) and the patterns of interacting species within ecological networks. ANINHADO is a program for researchers already familiarized with the nestedness concept and null model analysis. The degree of nestedness of a given binary matrix can be computed using distinct metrics. ANINHADO computes two of them: the recently-proposed NODF (Almeida-Neto et al. 2008) and the popular matrix s Temperature (T, Atmar & Paterson 1993). We strongly recommended the use of NODF to characterize the degree of nestedness due its theoretical consistence and its statistical behavior (Almeida-Neto et al. 2008). However, users may use T for compare his/her studied systems with published data.

50 modularity Barber, M. J Modularity and community detection in bipartite networks. Physical Review E 76: Guimerà R. and L.A.N. Amaral Functional cartography of complex metabolic networks. Nature 433: