Centre for Statistics in Ecology, Environment and Conservation Report 2018 - University of Cape Town
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Centre for Statistics in
Ecology, Environment
and Conservation
Report 2018
University of Cape Town
SEEC A NNUAL R EPORT 2018, U NIVERSITY OF C APE T OWN Rondebosch 7701, South Africa. http://www.seec.uct.ac.za/ https://twitter.com/SEEC_UCT https://www.facebook.com/SEEC.UCT Published 17 July 2019
Table of Contents 1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.1 Highlights of 2018 5 1.2 Projects and research interests of the group 6 1.2.1 Seasonality in the Cape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 1.2.2 SeaSearch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.2.3 Marine benthic ecology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.2.4 BioGaps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.2.5 Occupancy modelling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.2.6 Population demography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.2.7 Capture-Mark-Recapture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.3 The team 9 1.3.1 Core team . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.3.2 Postgraduate students . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 1.3.3 Advisory Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 1.3.4 Affiliates and partners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 2 Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.1 Research and capacity building 12 2.1.1 Metrics of performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.1.2 Students graduated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2.2 Co-publication 14 2.3 Student supervision 14
4
3 Partner organisations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.1 Within UCT 18
3.2 National 18
3.3 International 19
4 Outreach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.1 SEEC Stats Toolbox Seminars 20
4.2 Workshops 21
4.2.1 Model-based multivariate analysis of abundance data using R . . . . . . . . . . . . 21
4.2.2 SEEC-ACCESS Introduction to statistical modelling and data analysis course (18-20
July) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
4.3 African Bioacoustics Conference 22
4.4 Social media 22
4.5 SEEC student symposium 2018 22
4.6 Advisory boards 22
5 Funding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6 Publications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
7 Other research outputs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
7.1 Conferences 28
7.1.1 Posters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
7.1.2 Talks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
1. Summary
1.1 Highlights of 2018
This year was an eventful year for SEEC with, among many things, contributions to SANBI’s
BioGaps project, the hosting of David Warton who ran a course on multivariate data analysis, the
successful organisation of the inaugural African Bioacoustics Community conference, and a number
of high impact publications coming out.
Fracking in the Karoo now seems less likely to happen but the threat highlighted how little we
knew about the distribution of species that make up biodiversity in the large arid tracts of South Africa.
SEEC collaborated with the South African National Biodiversity Institute on the BioGaps project,
which aimed at quantifying biodiversity patterns across parts of the Karoo. SEEC was involved with
developing the sampling design and – as data started to come in – with the analysis of distribution
data. Postdoc Dominic Henry developed hierarchical occupancy models diverse taxonomic groups,
including butterflies, scorpions, reptiles, birds and more. Coming up with sampling protocols that
were both feasible in the field and allowed us to account for the ever-present detection process was a
challenge. We tested protocols that used time to first detection of a species and learned a lot about
different types of occupancy models. We also had to be creative about how to combine data collected
under different protocols and became fans of data fusion techniques.
The inaugural African Bioacoustics Community conference was organised and run by our very
own Tess Gridley. The conference was a massive success, attracting 130 participants from across
the globe and hosting eminent speakers such as Doug Gillespie, the creator of the well-known
PAMGuard software.
The Cape peninsula is home to Rose’s mountain toad (Capensibufo rosei), which occurs nowhere
else in the world. But who knew that this species also has an unusual and surprising life history?
A few years ago, then Honours student Francois Becker analysed survival of these toads, using
capture-mark-recapture data. He found a very strong relationship between rainfall and demography:
6 Chapter 1. Summary
survival strongly declined with increasing rainfall, whereas in years with lots of rain, the toads stayed
at the breeding puddles longer and apparently spent more resources reproducing than in dry years.
These results suggest an unusual degree of life-history plasticity that is tightly linked to weather.
Last year, these findings were finally published in the prestigious journal, American Naturalist
[3].
1.2 Projects and research interests of the group
1.2.1 Seasonality in the Cape
In March 2018 we heard that we had been successful in securing almost R9 M NRF funding for a
three-year Alliance for Collaboration on Climate & Earth Systems Science (ACCESS) grant. This
grant is supporting projects under seven themes at five different institutions (UCT, SAEON, Stellen-
bosch University, University of Venda and the CSIR) under the overarching theme of "Seasonality in
the Cape".
Climate change is likely to have much larger impacts in the Greater Cape Floristic Region
(GCFR) relative to the rest of the world. Climate models predict that temperatures will continue
to increase and that annual precipitation is likely to decrease over much of the GCFR. However,
what is less appreciated is that climate seasonality is also being affected, i.e. relative changes in
temperature and precipitation may be greater in a particular season relative to other seasons. For
example, maximum temperatures in autumn have been increasing at a relatively greater rate than in
other seasons across much of the GCFR. There is also some evidence to suggest that the winter rainy
season is starting later in the year. The effects of such changes in climate seasonality on biodiversity
1.2 Projects and research interests of the group 7
and ecosystem processes have been hardly investigated at all in this region.Our multi-institution,
multi-project NRF ACCESS “Seasonality in the Cape” program is making a start to address this
knowledge gap.
1.2.2 SeaSearch
Tess Gridley, who is part of our core team, is a founding director of Sea Search. Sea Search
conducts high quality, internationally recognised research in the southern African marine realm, with
a large focus on whales and dolphins. Tess has a particular interest in bioacoustics and published a
number of papers in this field [26, 17]. The research Sea Search does feeds into education and policy
recommendations.
1.2.3 Marine benthic ecology
Natasha Karenyi, one of our core team members and a lecturer in Biological Sciences, leads a marine
benthic ecology group in that department. She focus particularly on unconsolidated sediment habitats
and is also interested in marine biodiversity research, and utilising new or uncommon statistical
methods to analyse marine biodiversity data to answer ecological and conservation questions [19].
She also sits on SANBI’s Marine Ecosystem Classification Committee who is tasked with updating
the marine ecosystem classification and map for the National Biodiversity Assessment.
1.2.4 BioGaps
The Karoo is, for the most part, poorly surveyed for biodiversity, hampering efforts to prioritise
habitats for conservation. This is all the more concerning given that many new developments in
shale gas extraction, farming, mining, renewable energy infrastructure and the Square Kilometre
Array are planned for the Karoo.
8 Chapter 1. Summary
The SANBI BioGaps project was developed to address this shortcoming in biodiversity data and
SEEC has been involved from the start in developing this project. Res helped design the sampling
strategy and a number of our members have been involved in using occupancy modelling to develop
maps of species distributions to assist with prioritising areas for conservation.
1.2.5 Occupancy modelling
SEEC has a lot of expertise in this statistical method which uses species occurrences and predictors
of their occurrence and detectability to model a species’ probability of occurence and detectability.
As mentioned earlier, occupancy modelling conducted by SEEC members was pivotal in the BioGaps
project. Allan Clark is an expert in Bayesian methods for occupancy modelling. This year SEEC
published a number of papers using occupancy modelling [25? , 10? ]
1.2.6 Population demography
Res has been involved in modelling population demographics for many years now and continues to
use these skills to support a number of ecological questions and conservation measures [34, 33, 27, 3].
1.3 The team 9
1.2.7 Capture-Mark-Recapture
Capture-Mark-Recapture (CMR) models are well established and extensively used to estimate animal
abundance and demographic parameters of interest. More recently, incorporating spatial information
on where individuals are caught leads to Spatial Capture Recapture (SCR) models that are able to
estimate and model animal density. Greg Distiller, a core team member, did his PhD in these models
and has developed a continuous-time (CT) framework for spatial capture-recapture models that was
motivated by the emergence and growth of SCR data that are generated from camera trap surveys.
He currently supervises a number of students using SCR and CMR models, including Matthew
Rogan who is working on leopards in South Africa together with Panthera and the iCWild group.
1.3 The team
1.3.1 Core team
Res Altwegg UCT, Statistical Sciences (director)
David Borchers University of St Andrews, SEEC Honorary Research Associate (HRA)
Allan Clark UCT, Statistical Sciences
Jonathan Colville South African National Biodiversity Institute, SEEC HRA
Greg Distiller UCT, Statistical Sciences
Ian Durbach UCT, Statistical Sciences / African Institute for Mathematical Sciences / University of St Andr
Birgit Erni UCT, Statistical Sciences
Tess Gridley UCT, Statistical Sciences
Dominic Henry Endangered Wildlife Trust, SEEC HRA
Natasha Karenyi UCT, Biological Sciences
Sue Kuyper UCT, Administrator
Michelle Louw UCT, Biological Sciences, Technician
David Maphisa South African National Biodiversity Institute, SEEC HRA
Annalie Melin South African National Biodiversity Institute, SEEC HRA
Mzabalazo Ngwenya UCT, Statistical Sciences
Kirsten Packer UCT, Statistical Sciences, NRF Intern
Theoni Photopoulou University of St Andrews, SEEC
Sulaiman Salau UCT, Statistical Science
Jasper Slingsby South African Environmental Observation Network, SEEC HRA
Vernon Visser UCT, Statistical Sciences and ACDI
Henning Winker Department of Agriculture, Fisheries and Forestry, SEEC HRA
10 Chapter 1. Summary
1.3.2 Postgraduate students
Ph.D.
Gordon Botha Statistical Sciences
Francisco Cervantes Peralta Statistical Sciences
Greg Duckworth Statistical Sciences, graduated Dec 2018
Emmanuel Kabunga Statistical Sciences
Emma Lockerbie Biological Sciences, graduated 2018
Alecia Nickless Statistical Sciences, graduated Dec 2018
Ariella Rink Statistical Sciences
Matthew Rogan Biological Sciences
Kim Stevens Biological Sciences
Jessleena Suri Statistical Sciences
Zoe Woodgate Biological Sciences
M.Sc.
Luther Adams Biological Sciences
Gciniwe Dlamini Statistical Sciences, graduated Dec 2018
Peter Ivey Statistical Sciences
Maphale Matlala Statistical Sciences
Thina Ncube Biological Sciences
Leila Nefdt Biological Sciences
Jenicca Poongavanan Statistical Sciences
Hons
Reetumetse Tlhakung Statistical Sciences, graduated Dec 2018
Vhonani Tsanwani Statistical Sciences, graduated Dec 2018
Jolando Njati Statistical Sciences, graduated Dec 2018
Tessa Lloyd Statistical Sciences, graduated Dec 2018
Saiheal Narayan Statistical Sciences, graduated Dec 2018
Deepika Autar Statistical Sciences, graduated Dec 2018
Romelon Chetty Statistical Sciences, graduated Dec 2018
Matthew de Vries Statistical Sciences, graduated Dec 2018
Andile Gigaba Statistical Sciences, graduated Dec 2018
Sasha Paules Statistical Sciences, graduated Dec 2018
Morne Valentine Statistical Sciences, graduated Dec 2017
Alungile Gcaza Statistical Sciences, graduated Feb 20181.3 The team 11
1.3.3 Advisory Board
Susan Bourne UCT, Dean of the Science Faculty
Francesca Little UCT, HOD Department of Statistical Sciences
Muthama Muasya UCT, HOD Department of Biological Sciences
Bob Scholes University of the Witwatersrand
John Donaldson South African National Biodiversity Institute
1.3.4 Affiliates and partners
Affiliates
Raquel Garcia Stellenbosch University
Fitsum Abadi Gebreselassie New Mexico State University
Astrid Jarre UCT, Biological Sciences
Silvia Mecenero South African National Biodiversity Institute
Etienne Pienaar UCT, Statistical Sciences
Chevonne Reynolds University of the Witwatersrand
Peter Ryan UCT, Biological Sciences
Partner academics
Iain MacDonald UCT, Actuarial Science
Guy Midgley Stellenbosch University
Les Underhill UCT, Biological Sciences2. Research
2.1 Research and capacity building
2.1.1 Metrics of performance
SEEC members produced 40 publications in 2018, which means an average of 2.28 publications per
SEEC core member. Mean publication impact factor was 2.98.
Table 2.1: Research performance across years
Year # publications # per core member Mean impact factor
2018 40 2.28 2.98
2017 46 3.28 3.81
2016 49 2.43 3.21
2015 41 2.16 3.462.1 Research and capacity building 13
2.1.2 Students graduated
• Greg Duckworth graduated with a PhD. In his thesis – entitled "Effects of Protected Areas and
Climate Change on the Occupancy Dynamics of Common Bird Species in South Africa".
Greg used occupancy models and data from the Southern African Bird Atlas Project to examine
which bird species benefitted from protected areas. He found that insectivorous species tended
to occur in protected areas at higher densities than outside, whereas granivorous species fared
relatively better outside protected areas [? ]. Greg received his PhD certificate after a long
graduation ceremony – it was dark outside when we left UCT’s Sarah Baartman hall – on 14
December.
• Alecia Nickless and Emma Lockerbie also graduated with a PhD in 2018. Alecia did her
PhD in the Stats deparment and her thesis was entitled "Regional CO2 flux estimates for14 Chapter 2. Research
South Africa through inverse modelling". Emma Lockerbie did her PhD under the supervision
of Lynne Shannon and Astird Jarre in the MARE group and her thesis was entitled "A
decision tree framework for assessing status of exploited marine ecosystems under changing
environmental conditions".
• Gciniwe Dlamini received her MSc for her project entitled "Machine learning methods for
individual acoustic recognition in a species of field cricket".
2.2 Co-publication
As a measure of current collaboration within the core team, we plotted 2018 publications that were
co-authored between SEEC core members. In the figure below, the lines between team member’s
names represent joint publications.
2.3 Student supervision
SEEC trained 11 PhD, 7 Masters and 12 Honours students during 2018. Of these, 3 PhD students, 1
Masters student and all the Honours students graduated during the year.
As another measure of collaboration within SEEC, we plotted co-supervision of postgraduate
students (MSc and PhD). Thin lines connecting team member’s names indicate joint supervision of2.3 Student supervision 15 one student; thick lines represent co-supervision of two students.
3. Partner organisations We have a strong network of partners at three levels: within UCT (depicted below with a connecting semicircle), nationally, and internationally.
17
18 Chapter 3. Partner organisations
EGS
3.1 Within UCT
A number of SEEC members, Res Altwegg, Birgit Erni, David Maphisa, Mzabalazo Ngwenya,
Jasper Slingsby and Vernon Visser, are partners with researchers in the Department of Biological
Sciences and Environmental and Geographical Sciences on an NRF ACCESS-funded project,
"Seasonality in the Cape". SEEC members collaborate with many other researchers in Biological
Sciences, particularly with the FitzPatrick Institute for African Ornithology, the Plant Conser-
vation Unit, and the Institute for Communities and Wildlife in Africa. Vernon Visser holds a
research fellowship with the African Climate and Development Initiative.
3.2 National
A key partner outside UCT is the South African National Biodiversity Institute. Three SANBI
scientists, Jonathan Colville, Annalie Melin and David Maphisa, are SEEC core members. In
addition, Natasha Karenyi serves on SANBI’s Marine Ecosystem Classification Committee (MECC)
and Greg Distiller serves on the Leopard Monitoring Committee. South African Environmental
Observation Network’s Jasper Slingby is a SEEC core member. Former SEEC postdoc Dominic
Henry took up a position as ecological modelling specialist with the Endangered Wildlife Trust.3.3 International 19
SEEC core member Henning Winker is a fisheries scientist in the Department of Agriculture,
Forestry and Fisheries.
Guy Midgley from Stellenbosch University’s Department of Botany and Zoology is a SEEC
partner. SEEC has several ongoing collaborations, and has signed a memorandum of understanding,
with the Centre for Invasion Biology at the University of Stellenbosch. SEEC also collaborates
with the Department of Geography & Environmental Studies, particularly Prof. Helen De Klerk.
Stefan Foord at the University of Venda and his MSc student, Ratshibvumo Tshikambu, are
part of SEEC’s NRF ACCESS project.
We work with key conservation organisations: Cape Nature, the Endangered Wildlife Trust,
and BirdLife South Africa on various projects.
3.3 International
Internationally, we collaborate with some of the leading groups in our field. One of them is the
Centre for Research into Ecological and Environmental Modelling (CREEM) at the University
of St Andrews. David Borchers from CREEM is a SEEC core member, Theoni Photopoulou is
currently at CREEM as a Newton International Fellow and Ian Durbach has taken up a position
at CREEM during 2018. We have an ongoing collaboration with Colin Beale at the University of
York on analysing spatial biodiversity data and with Jim Nichols at the Patuxent Wildlife Research
Centre of the USGS on using occupancy models for citizen science data. David Warton from the
University of New South Wales visited SEEC in January 2018.4. Outreach
4.1 SEEC Stats Toolbox Seminars
The SEEC Stats Toolbox Seminars were once again very successful in 2018, with another eight talks
added to our growing collection. The material (slides, R code, example data files) are available on our
web site (seec.uct.ac.za/stats-toolbox-seminars) for all of these seminars. We live-stream
the seminars to enable people to participate who cannot physically attend the seminar. The seminars
are also recorded and can be watched from our web site.4.2 Workshops 21
4.2 Workshops
4.2.1 Model-based multivariate analysis of abundance data using R
In January SEEC hosted David Warton, a Professor and Australian Research Council Future Fellow
from the University of South Wales and leader of the Ecostats research group http://web.maths.
unsw.edu.au/~dwarton/
David champions the movement away from traditional methods of exploratory multivariate
analyses to more predictive and testable model-based analyses in an effort to maintain the integrity
of the data during analyses. To this end he has developed the mvabund R package.
While at UCT, David taught a model-based multivariate statistics course from 22-26 January
attended by 35 ecologists and statisticians from all over South Africa. This course challenged our
thinking about popular multivariate methods and introduced new methodologies which will hopefully
become more common in ecology.22 Chapter 4. Outreach
4.2.2 SEEC-ACCESS Introduction to statistical modelling and data analysis course (18-20
July)
SEEC members ran a condensed version of the STA2007/5014 course on behalf of ACCESS, which
was attended by around 60 people. Feedback from the course participants was generally very positive.
As a result of this success, SEEC has decided to run the course again in 2019.
4.3 African Bioacoustics Conference
Tess Gridley organised and ran this inaugural conference which was held from 2-7 December at
UCT and supported by SEEC and the Department of Statistical Sciences. The conference was a
massive success, attracting 130 participants from across the globe.
4.4 Social media
SEEC is now followed by 524 people on Twitter and 158 on Facebook (on 15 May 2019).
4.5 SEEC student symposium 2018
The annual SEEC Student Symposium was held on 28 May 2018 in the Postgraduate Student Room
in the Otto Beit building. Sheona Schackleton (deputy director of the ACDI) presented the plenary
and 13 SEEC students presented on their work.
This symposium continues to be an important event for promoting SEEC to a wider UCT
audience and for learning about each other’s work.
4.6 Advisory boards
Res Altwegg serves on the steering committee for SANBI’s BioGaps project and for the Southern
African Bird Atlas Project.5. Funding • Res Altwegg, Vernon Visser, Mzabalazo Ngwenya, David Maphisa, Birgit Erni, Jasper Slingsby - NRF ACCESS Annual Cycle and Seasonality grant of R8,500,000 (2018-2021) • Jasper Slingsby, Vernon Visser, Res Altwegg - NRF SASSCAL grant of R2,155,000 (2019- 2021) • Vernon Visser - ACDI Fellowship support of R300,000 • Natasha Karenyi, Allan Clark - NRF Marine and Coastal Research grant of R1,325,000 (2019-2021)
6. Publications
[1] A. Amar, R. Buij, J. Suri, P. Sumasgutner, and M.Z. Virani. Conservation and ecology of
African raptors. In J. Sarasola, J. Grande, and J. Negro, editors, Birds of Prey, pages 419–455.
Springer, Cham, 2018. ISBN 978-3-319-73745-4.
[2] D.A. Barraclough, J.F. Colville, F. Karolyi, and H.W. Krenn. A striking new species
of Prosoeca Schiner, 1867 (Diptera: Nemestrinidae): An important pollinator from the
Bokkeveld Plateau, Northern Cape Province, South Africa. Zootaxa, 4497(3):411–421, 2018.
doi:10.11646/zootaxa.4497.3.5.
[3] F.S. Becker, K.A. Tolley, G.J. Measey, and R. Altwegg. Extreme climate-induced life-
history plasticity in an amphibian. The American Naturalist, 191(2):250–258, 2018.
doi:10.1086/695315.
[4] T.C. Bonebrake, C.J. Brown, J.D. Bell, J.L. Blanchard, A. Chauvenet, C. Champion, I-C.
Chen, T.D. Clark, R.K. Colwell, . Danielsen, and others. Managing consequences of climate-
driven species redistribution requires integration of ecology, conservation and social science.
Biological Reviews, 93(1):284–305, 2018. doi:10.1111/brv.12344.
[5] M.S. Burman, L.G Underhill, R. Altwegg, B. Erni, M. Remisiewicz, and J. MacLeod. Migratory
connectivity of barn swallows in South Africa to their Palaearctic breeding grounds. Diversity
and Distributions, 24(11):1699–1708, 2018. doi:10.1111/ddi.12810.
[6] J.F. Colville, M.D. Picker, and R.M. Cowling. Feeding ecology and sexual dimor-
phism in a speciose flower beetle clade (Hopliini: Scarabaeidae). PeerJ, 6:e4632, 2018.
doi:10.7717/peerj.4632.
[7] H.M. de Klerk, N.D. Burgess, and V. Visser. Probabilistic description of vege-
tation ecotones using remote sensing. Ecological Informatics, 46:125–132, 2018.
doi:10.1016/j.ecoinf.2018.06.001.25
[8] M.L. Dicken, H. Winker, M.J. Smale, and G. Cliff. Sharks caught in the KwaZulu-
Natal bather protection programme, South Africa. 14. The smooth hammerhead shark
Sphyrna zygaena (Linnaeus). African Journal of Marine Science, 40(2):157–174, 2018.
doi:10.2989/1814232X.2018.1470031.
[9] M. Dornelas, L.H. Antao, F. Moyes, A.E. Bates, A.E. Magurran, D. Adam, A.A. Akhmet-
zhanova, W. Appeltans, J.M. Arcos, H. Arnold, and others. BioTIME: A database of biodiversity
time series for the Anthropocene. Global Ecology and Biogeography, 27(7):760–786, 2018.
doi:10.1111/geb.12729.
[10] M. Drouilly, A. Clark, and M. J. O’Riain. Multi-species occupancy modelling of mammal
and ground bird communities in rangeland in the Karoo: a case for dryland systems globally.
Biological conservation, 224:16–25, 2018. doi:10.1016/j.biocon.2018.05.013.
[11] G.D. Duckworth and R. Altwegg. Effectiveness of protected areas for bird conservation
depends on guild. Diversity and Distributions, 24(8):1083–1091, 2018. doi:10.1111/ddi.12756.
[12] I. Durbach and G. Montibeller. Predicting in shock: on the impact of negative, extreme, rare,
and short lived events on judgmental forecasts. EURO Journal on Decision Processes, 6(1):
213–233, 2018. doi:10.1007/s40070-017-0063-2.
[13] F. Forest, J. Colville, and R. Cowling. Evolutionary diversity patterns in the Cape flora of South
Africa: applications and challenges in biodiversity science. In R. Scherson and D. Faith, editors,
Phylogenetic Diversity: Applications and Challenges in Biodiversity Science, pages 167–187.
Springer, Cham, 2018. ISBN 978-3-319-93145-6. doi:10.1007/978-3-319-93145-6_9.
[14] R. Froese, H. Winker, G. Coro, N. Demirel, A.C. Tsikliras, D. Dimarchopoulou, G. Scar-
cella, W.N. Probst, M. Dureuil, D. Pauly, and others. A new approach for estimating stock
status from length frequency data. ICES Journal of Marine Science, 75(6):2004–2015, 2018.
doi:10.1093/icesjms/fsy078.
[15] R. Froese, H. Winker, G. Coro, N. Demirel, A.C. Tsikliras, D. Dimarchopoulou, G. Scarcella,
M. Quaas, and N. Matz-Lück. Status and rebuilding of European fisheries. Marine Policy, 93:
159–170, 2018. doi:10.1016/j.marpol.2018.04.018.
[16] T. Gridley, S.H. Elwen, G. Harris, D.M. Moore, A.R. Hoelzel, and F. Lampen. Hy-
bridization in bottlenose dolphins—A case study of Tursiops aduncus T. truncatus hy-
brids and successful backcross hybridization events. PLOS ONE, 13(9):1–15, 2018.
doi:10.1371/journal.pone.0201722.
[17] T. Gridley, M.F.F. Silva, C. Wilkinson, S.M. Seakamela, and S.H. Elwen. Song recorded near a
super-group of humpback whales on a mid-latitude feeding ground off South Africa. The Jour-
nal of the Acoustical Society of America, 143(4):EL298–EL304, 2018. doi:10.1121/1.5032126.
[18] A. Jarre, L.J. Shannon, R. Cooper, G.L. Duggan, L.C. Gammage, E.M. Lockerbie, E.S.
McGregor, S.M. Ragaller, N. Visser, C. Ward, and others. Untangling a Gordian knot that must
not be cut: social-ecological systems research for management of southern Benguela fisheries.
Journal of Marine Systems, 188:149–159, 2018. doi:10.1016/j.jmarsys.2018.01.004.26 Chapter 6. Publications
[19] N. Karenyi, K. Sink, R. Nel, A.E. Clark, and R. Altwegg. Imperfect detection distorts depth-
related trends in marine macrofaunal species richness. Ecography, 41(10):1698–1706, 2018.
doi:10.1111/ecog.03439.
[20] K.V. Katsikopoulos, I.N. Durbach, and T.J. Stewart. When should we use simple de-
cision models? A synthesis of various research strands. Omega, 81:17 – 25, 2018.
doi:10.1016/j.omega.2017.09.005.
[21] A. Ke, M.D. Sibiya, C. Reynolds, R.A. McCleery, A. Monadjem, and R.J. Fletcher. Landscape
heterogeneity shapes taxonomic diversity of non-breeding birds across fragmented savanna
landscapes. Biodiversity and conservation, 27(10):2681–2698, 2018. doi:10.1007/s10531-018-
1561-7.
[22] A.A. Kock, T. Photopoulou, I. N. Durbach, K. Mauff, M. Meÿer, D. Kotze, C.L. Griffiths,
and M.J. O’Riain. Summer at the beach: spatio-temporal patterns of white shark occur-
rence along the inshore areas of False Bay, South Africa. Movement ecology, 6(1):7, 2018.
doi:10.1186/s40462-018-0125-5.
[23] M.C. LaScaleia, C. Reynolds, C.N. Magagula, F. Roets, and R.A. McCleery. Dung bee-
tle richness decreases with increasing landscape structural heterogeneity in an African
savanna-agricultural mosaic. Insect Conservation and Diversity, 11(4):396–406, 2018.
doi:10.1111/icad.12290.
[24] K.J. Lloyd, R. Altwegg, C. Doutrelant, and R. Covas. Factors affecting the foraging distance
and duration of a colonial bird, the sociable weaver, in a semi-arid environment. African
Journal of Ecology, 56(3):659–663, 2018. doi:10.1111/aje.12484.
[25] D.H. Maphisa, H. Smit_Robinson, and R. Altwegg. Dynamic multi-species occupancy models
of birds of high-altitude grasslands in eastern South Africa. PeerJ Preprints, 6:e26932v1, 2018.
doi:10.7287/peerj.preprints.26932v1.
[26] M.J. Martin, T. Gridley, S.H. Elwen, and F.H. Jensen. Heaviside’s dolphins (Cephalorhynchus
heavisidii) relax acoustic crypsis to increase communication range. Proceedings of the Royal
Society B: Biological Sciences, 285(1883):20181178, 2018. doi:10.1098/rspb.2018.1178.
[27] G.T.W. McClelland, R. Altwegg, R.J. van Aarde, S. Ferreira, A.E. Burger, and S.L. Chown.
Climate change leads to increasing population density and impacts of a key island invader.
Ecological Applications, 28(1):212–224, 2018. doi:10.1002/eap.1642.
[28] A. Melin, M. Rouget, J.F. Colville, J.J. Midgley, and J.S. Donaldson. Assessing the role of
dispersed floral resources for managed bees in providing supporting ecosystem services for
crop pollination. PeerJ, 6:e5654, 2018. doi:10.7717/peerj.5654.
[29] A.Y.A. Mukhtar, J.B. Munyakazi, R. Ouifki, and A.E. Clark. Modelling the effect of
bednet coverage on malaria transmission in South Sudan. PLOS ONE, 13(6):1–22, 2018.
doi:10.1371/journal.pone.0198280.
[30] M. Murgatroyd, T. Photopoulou, L.G. Underhill, W. Bouten, and A. Amar. Where eagles soar:
fine-resolution tracking reveals the spatiotemporal use of differential soaring modes in large
raptor. Ecology and Evolution, 8(13):6788–6799, 2018. doi:10.1002/ece3.4189.27
[31] A. Nickless, P.J. Rayner, B. Erni, and R.J. Scholes. Comparison of the genetic algorithm
and incremental optimisation routines for a Bayesian inverse modelling based network design.
Inverse Problems, 34(5):055006, 2018. doi:10.1088/1361-6420/aab46c.
[32] K.V. Nkuna, V. Visser, J.R.U. Wilson, and S. Kumschick. Global environmental and socio-
economic impacts of selected alien grasses as a basis for ranking threats to South Africa.
NeoBiota, 41:19, 2018. doi:10.3897/neobiota.41.265.
[33] W.C. Oosthuizen, R. Altwegg, M. Nevoux, M.N. Bester, and P.J.N. de Bruyn. Phenotypic
selection and covariation in the life-history traits of elephant seals: heavier offspring gain a
double selective advantage. Oikos, 127(6):875–889, 2018. doi:10.1111/oik.04998.
[34] A. Payo-Payo, A. Sanz-Aguilar, D. Gaglio, R.B. Sherley, T.R. Cook, R. Altwegg, and P.G.
Ryan. Survival estimates for the greater crested tern Thalasseus bergii in southern Africa.
African Journal of Marine Science, 40(1):43–50, 2018. doi:10.2989/1814232X.2018.1437470.
[35] T. Photopoulou. Human footprint restricts ranges. Nature ecology & evolution, 2(5):773, 2018.
doi:10.1038/s41559-018-0538-y.
[36] H.M. Poulos, A.M. Barton, J.A. Slingsby, and D.M.J.S. Bowman. Do mixed fire
regimes shape plant flammability and post-fire recovery strategies? Fire, 1(3):39, 2018.
doi:10.3390/fire1030039.
[37] C. Reynolds, R.J. Fletcher, C.M. Carneiro, N. Jennings, A. Ke, M.C. LaScaleia, M.B. Lukhele,
M.L. Mamba, M.D. Sibiya, J. D. Austin, and others. Inconsistent effects of landscape hetero-
geneity and land-use on animal diversity in an agricultural mosaic: a multi-scale and multi-taxon
investigation. Landscape ecology, 33(2):241–255, 2018. doi:10.1007/s10980-017-0595-7.
[38] C. Swart, V. Visser, and T.B. Robinson. Patterns and traits associated with invasions by
predatory marine crabs. NeoBiota, 39:79, 2018. doi:10.3897/neobiota.39.22002.
[39] J.T. Thorson, M.B. Rudd, and H. Winker. The case for estimating recruitment caria-
tion in data-moderate and data-poor age-structured models. Fisheries Research, 2018.
doi:10.1016/j.fishres.2018.07.007. In Press, Corrected Proof.
[40] H. Winker, F. Carvalho, and M. Kapur. JABBA: Just Another Bayesian Biomass Assessment.
Fisheries Research, 204:275–288, 2018. doi:10.1016/j.fishres.2018.03.010.
[41] Z. Woodgate, G. Distiller, and J. O’Riain. Variation in mammal species richness and relative
abundance in the Karoo. African Journal of Range & Forage Science, 35(3-4):325–334, 2018.
doi:10.2989/10220119.2018.1522513.7. Other research outputs
7.1 Conferences
7.1.1 Posters
1. Van Blerk, J., A. West, T. Hoffmann, R. Altwegg. The effects of rainfall seasonality on
post-fire vegetation dynamics in the GCFR. Fynbos Forum, 31 Jul - 3 Aug 2018, Goudini.
7.1.2 Talks
1. Altwegg, R., G.J. Measey, D.L. Borchers and B.C. Stevenson. Estimating density, occupancy
and species richness from acoustic data. African Bioacoustics Community Conference, 6
December 2018, University of Cape Town.
2. Altwegg, R., J. Prokosch, S.E. Piper, Z. Bernitz, H. Bernitz, and B. Erni. Are animals shrinking
due to climate change? Temperature mediated selection on body mass in mountain wagtails.
International Statistical Ecology Conference, 2 July 2018, St Andrews, UK.
3. Henry, D and R. Altwegg. Using time-to-detection models to quantify patterns of biodiversity
in the Karoo. International Statistical Ecology Conference, 5 July 2018, St Andrews, UK.
4. Slingsby, J., G.R. Moncrieff, A.J. Potts, and A.M. Wilson. Tools for monitoring vegetation
from space. 2018 Thicket Forum, 12 June 2018, Addo Elephant National Park.
5. Slingsby, J., G.R. Moncrieff, and A.M. Wilson. A near-real time satellite tool for monitoring
and mapping ecological impacts in Fynbos. Biodiversity Planning Forum 2018, 19-22 June
2018, Cape St Francis.
6. Suri, J., R. Altwegg, P. Anderson, and R. Thomson. How do cities structure bird communities
in time and space. URBIO 2018: Urban Biodiversity & Food Security, 12 September 2018,
Cape Town.
7. Visser, V, R. Chetty, M. De Vries, J. Van Blerk, M. Louw, K. Atkins, J. Suri, and R. Tshikambu.7.1 Conferences 29
Seasonality in the Cape. 4th South African National Global Change Conference, 3-6 December,
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