1. FINAL PUBLISHABLE SUMMARY REPORTUnderstanding how the plants and animals that live in the seafloor vary in their spatial

patterns of diversity and abundance is fundamental to improving knowledge of ecological

processes that underpin communities, as well as advance the modelling of species

distributions under realistic assumptions. Such critical knowledge, which was gathered during

this project, informs both our fundamental understanding of ecosystem processes and

community ecology, ecological monitoring, as well as the role of biodiversity in maintaining

ecosystem functioning in coastal ecosystems.

1200 macrobenthic samples were collected (Objective 1) in Manukau, Tauranga, and

Kaipara Harbour, New Zealand, following a pre-determined sampling scheme (Fig. 1). We

identified over 145 species, mostly bivalves, polychaetes, and crustaceans living beneath the

surface of the intertidal sands, and counted 73813 individuals. In addition, 960 Chlorophyll a

samples as a proxy for food availability were analysed, 960 sediment samples to caption

habitat variability were processed, and 960 photo-quadrats of the sampling locations were

used to describe cover of seasgrass (Zostera), shellhash, and bare sand.

Fig. 1. Sampling design (top panel), encompassing 400 sampling stations, which are positioned to match a

number of spatial lags ranging from 0.3 m to 1000 m. Illustrated are the abundances of Macomona liliana

(scaled dots; 0-40 ind./core) at Kaipara Harbour. The background displays a seascape of median grain size

(darker grey indicates coarser sands; values range between 170-250 µm). Bottom panels show a sampling area

at low tide.

Using recent multivariate spatial models (Moran’s Eigenvector Mapping; MEM), we found

that benthic communities were distinctly spatially structured at four spatial scales (see Fig. 2),

but there was no clear separation of the importance of environmental vs. biotic factors at

these scales (Objective 2). A broad selection of environmental variables contributed to the

large-scale variation, whereas a much-limited set explained part of the fine-scale community

structure. Our results emphasize there is no prevailing scale to which environmental factors

drive biodiversity and stress the importance of dissecting variation across scale to advance an

understanding of processes structuring species communities and inform conservation

measures.

Fig 2. Range of spatial autocorrelation of each significant positive MEM variable. Broad: MEM variables with a

range > 100 m; Meso: MEM variables with a range < 100 m and > 50 m; Small: MEM variables with a range <

50 m and > 15 m; Fine: MEM variables with a range < 15 m.

Also, we used recently developed so-called Joint Species Distribution Models (Objective 3),

to accommodate both spatial correlations within and between locations and give full

inference about model parameters and the characteristics of unobserved spatially structured

factors. Key is that such models enable to separate shared habitat preferences from co-

occurrence patterns due to interactions, such as competition. We demonstrated the utility of

these models in defining the role of species interactions across large spatial scales. Our

results show the presence of species interactions beyond scales generally amenable to

manipulative studies and provide a new approach allowing conservation research and

measures to acknowledge and assess important ecological phenomena.

Furthermore, it is well recognized that the functional performance of individual

species is affected by abundance and distribution, but the implication for multiple species that

share traits influencing functional redundancy and resilience to stressors has not been

resolved. Therefore, we assessed the degree of sharing of specific functional traits in these

communities. We defined functional groups, based on biological traits that relate to how

macrofauna modify sediment biogeochemistry and stability, and their resilience to

disturbance. Results (Fig. 3) show clear spatial gradients and boundaries of abundance and

distributions separating function. Our findings emphasise the importance of not only within

functional group species richness, but also abundance and occurrence as a framework to

investigate functional diversity and resilience of benthic seafloor communities.

Fig. 3. Left spatial distribution of functional groups based on interpolated (log-transformed) abundances (filled

contours; darker shading denotes higher abundances; range 0 to 2.1) and functional group richness (scaled

points; larger points indicate higher richness; the largest number of co-occurring species within a functional

group is 6 species. Right: correlograms, based on functional group abundance, illustrate (a) a gradient, (b) a

large patch and (c) multiple patches. Filled symbols denote significant Moran’s I values.

2. USE AND DISSEMINATION OF FOREGROUNDSection A (public) – DISSEMINATION MEASURES

PublicationsA number of publications are currently in preparation or under review and will therefore only be available after the project has ended.

Kraan C, Greenfield BL, Dormann CF & Thrush SF. 2015. Scale-dependent biodiversity composition in cryptic coastal sandflat communities. Public Library of Science ONE 10: e0142411.

Thrush SF, Kraan C, Hewitt JE & Loher AM. Habitat complexity and marine soft-substrate systems. In: Tokeshi M (ed). Habitat Complexity in Aquatic Systems: Ecological Perspectives. Springer. Accepted.

Greenfield BL, Kraan C*, Pilditch CA & Thrush SF. 2016. Mapping functional groups can provide insight into ecosystem functioning and potential resilience of intertidal sand flats. Marine Ecology Progress Series 548, 1-10. *corresponding author

Lohrer AM, Thrush SF, Hewitt JE & Kraan C. 2015. The up-scaling of ecosystem functions in a heterogeneous world. Scientific Reports 5, 10349.

Pratt DR, Pilditch CA, Lohrer AM, Thrush SF & Kraan C. 2015. Spatial distributions of grazing activity and microphytobenthos reveal scale-dependent relationships across a sedimentary gradient. Estuaries & Coasts 38, 722-734.

Calabrese JM, Certain G, Kraan C & Dormann CF. 2014. Stacking species distribution models and adjusting bias by linking them to macroecological models. Global Ecology & Biogeography 23, 99-112.

Thrush SF, Hewitt JE, Parkes S, Lohrer AM, Pilditch C, Woodin SA, Wethey DS, Chiantore M, Asnaghi V, de Juan S, Kraan C, Rodil I, Savage C & van Colen C. 2014. Experimenting with ecosystem interaction networks in search of threshold potentials in real world marine ecosystems. Ecology 95, 1451-1457.

Scientific communicationsThrush S, Hewitt J, Pilditch C, Douglas E, Lohrer AM, O’Meara T & Kraan C. 2015.

Infaunal bivalves and their role in biodiversity and ecosystem function relationships at the landscape scale. Coastal and Estuarine Research Federation. Portland, USA.

Douglas E, Pilditch C, Kraan C, Schipper L, Lohrer AM & Thrush SF. 2015. Biodiversity-ecosystem function relationships drive coastal denitrification – evidence from a real world ecosystem. Estuarine & Coastal Science Association. London, UK.

Andresen H, Thrush SF & Kraan C. 2015. Adult-juvenile associations in bivalves disentangled from environment. European Marine Biology Symposium. Helgoland, Germany.

Pratt D, Pilditch C, Lohrer AM, Thrush SF & Kraan C. 2015. Deposit feeding activity and microphyte biomass relationships across a benthic sediment gradient. European Marine Biology Symposium. Helgoland, Germany.

Douglas E, Pilditch C, Kraan C, Schipper L, Lohrer AM & Thrush SF. 2015. Macrobenthic community composition drives denitrifier response to nutrient loading. European Marine Biology Symposium. Helgoland, Germany.

Douglas E, Pilditch C, Kraan C, Schipper L, Lohrer AM & Thrush SF. 2015. Macrobenthic community composition drives denitrifier response to nutrient loading. New Zealand Marine Science Society conference. Auckland, New Zealand.

Kraan C, Greenfield BL, Dormann CF & Thrush SF. 2014. Spatial structuring of biodiversity. Ecological Society of Australia. Alice Springs, Australia.

Kraan C, Finley AO, Thrush SF, Piersma T & Dormann CF. 2014. Putting biotic interactions into distribution analysis. Ecological Society of America. Sacramento, USA.

Kraan C, Finley AO, Thrush SF, Piersma T & Dormann CF. 2014. Conservation strategies should encompass species interactions and spatial autocorrelation. Australian Marine Science Association. Canberra, Australia.

Hines L, Pilditch C, Kraan C, Lohrer D & Thrush SF. 2014. The effect of enhanced nutrient levels on coastal ecosystem functions. Golden Key International Summit, Boston, USA.

Thrush S, Hewitt J, Parks S, Lohrer D, Pilditch C, van Colen C, Woodin S, Wethey D, Chiantore M, Asnaghi V & Kraan C. Integrating causal and exploratory techniques to indicate threshold potentials in real world ecosystem dynamics. 2013. Coastal and Estuarine Research Federation. San Diego, USA.

Kraan C, A Finley, C Dormann & S Thrush. 2013. Spatial perspectives in ecology. New Zealand Marine Science Society conference. Hamilton, New Zealand.

Greenfield BL, C Pilditch, C Kraan, JE Hewitt & Thrush SF. 2013. Resilience of sandflats indicated by variation in functional group diversity. New Zealand Marine Science Society conference. Hamilton, New Zealand.

Networking activitiesParticipated in the workshop: Long-term Monitoring of Species Population Dynamics.

Frankfurt, Germany (2015)Invited lecture at Massey University, Palmerston North, New Zealand (2014)Invited to the workshop: Matrix of Marine Ecosystem Services. Auckland, New Zealand

(2014)Invited lecture at the University of Waikato, Hamilton, New Zealand (2013)Participating expert during the Miranda BioBlitz (2013).

Training activitiesParticipated in the workshop “Modelling the distribution of species and communities

accounting for detection using R and BUGS/JAGS”. IMEDEA, Spain (2016).Participated in the Eco-Stats Symposium/workshop: New opportunities at the interface

between ecology and statistics. Sydney, Australia (2013)

Section B (confidential) - EXPLOITABLE FOREGROUND AND PLANS FOR EXPLOITATIONNOT APPLICABLE

3. SCIENTIST IN CHARGE QUESTIONNAIRERESEARCH TRAINING ASSESSMENT:What is the size of the hosting research group?20 persons

How many researchers have you supervised, within the past 10 years? Of which funded by:EC/Marie Curie actions: 1EC Other Funding: 2University fellowships: 0National public bodies: 15Industry: 0Other: 2Other, please specify: Columbia, Egypt

How many researchers have you supervised within this project?1Corresponding to how many person months? 36

Number of publications resulting directly from the research project:Recruited researcher(s) and yourself: 2Recruited researcher(s) alone: 5Recruited researcher(s) with authors other than yourself: 5

Participation of the recruited researcher(s) at conferences (number):Passive: 1Active: 10How do you rate the overall success of the research training?Very successful

General assessment:The project was a success regarding attendance at conferences and number of publications. Note that more publications are currently under review, close to submission, or in preparation.

RESEARCHERS ASSESSMENT:Rate the overall level of the recruited researcher(s) integration in the research team and the host organisation with regards to:participation in meetings/seminars: Gooddiscussions of results and project-related topics: Excellentco-operation with other team members: Excellentco-operation with other researchers of the host institution: Not applicable, since my group represents the only group currently employing the models that are part of the project

Rate the overall performance of the recruited researcher(s) with regard to:capacity to develop new skills and to benefit from training: Excellentproductivity (research results/publications/international conference attendance): Excellentcommunication skills: Excellentgroup leader skills (collaboration with other groups/project management): Excellenttraining and/or teaching skills: In New Zealand Excellent, in Freiburg there was no opportunity for thisComment:Skills related to group leadership, training of others, and project management were particularly relevant during the outgoing phase and executed in an excellent fashion. This was less relevant during the return phase and therefore hard to rate

RESEARCH TRAINING OUTCOMES:Has this project provided additional links with other research groups or institutions? YesIf yes, indicate the number of contacts in each caseUniversities 3Research Centres 1Industry/private companies 0Others 0If Other, please specify:

Rate the importance of the following outcomes of the research training:results of the research: Importantnumber of publications: Most importantdevelopment of research: Importantestablishment of international collaborations: Importanttransfer of knowledge/technology: Importanttraining of students/researchers: Importantfurther academic qualifications (PhD, habilitation etc.) for fellows: less importantComments:It is difficult to judge the research training, since its impact is only clear after the project has ended. However, the fellow has recently secured a Marie-Curie European Fellowship, which supports the critical impact these grants have on building an attractive resume and career prospects.

YOUR OPINION ABOUT THE MARIE CURIE ACTIONS:Comments:Did you have previous knowledge of the Marie Curie actions? YesIf yes, what sort of image do you think that the Marie Curie actions have among the scientificcommunity in your research area?Receiving a MC Grant is considered a major achievement and an important accolade to a resume.