CIE Spotlight: Making a New Dog?

Thomas N., Tim D. and Euan R.

Authors: Thomas M. Newsome, Peter J. S. Fleming, Christopher R. Dickman, Tim S. Doherty, William J. Ripple, Euan G. Ritchie & Aaron J. Wirsing

Source: BioScience, 67, (4):374-381, 05 April 2017

Brief summary of the paper: We are in the middle of a period of rapid and substantial environmental change. One impact of this upheaval is increasing contact between humans and other animals, including wildlife that take advantage of anthropogenic foods.

As a result of increased interaction, the evolution and function of many species may be altered through time via processes including domestication and hybridization, potentially leading to speciation events.

We discuss the ecological and management importance of such possibilities, using gray wolves and other large carnivores as case studies. We identify five main ways that carnivores might be affected: changes to social structures, behavior and movement patterns, changes in survivorship across wild- to human-dominated environments, evolutionary divergence, and potential speciation.

As the human population continues to grow and urban areas expand while some large carnivore species reoccupy parts of their former distributions, there will be important implications for human welfare and conservation policy.

More info available via Deakin Research.

CIE Seminar Series 2017 – Apex predators and the global extinction crisis: advances in theory and future research

Thomas N.

SPEAKER: Dr Thomas Newsome, Alfred Deakin Postdoctoral Research Fellow, Centre for Integrative Ecology/School of Life and Environmental Sciences, Deakin University

DATE: Friday, 28th April 2017
LOCATION: Melbourne Campus at Burwood – Burwood Corporate Centre (attendees-please report to reception for room details on the day)
TIME: 1:30pm
Seminar will also be video linked to the following campuses: Geelong Campus at Waurn Ponds – room ka4.207; and Warrnambool Campus, Room B3.03

External visitors – wish to join us and connect to our seminars?

  • You may connect to the live seminar via *N SEBE VMP LES Seminars [ID.36958] or via the methods listed HERE.
  • For Deakin staff and students, please join via Skype for Business (Lync).
  • Could not log in? More info on how to connect is available HERE.
  • Please note that connection is only available while a seminar is taking place.

As a courtesy, we request that when connecting to the seminar that you mute your microphone unless you are required to speak, this would ensure that the sound from the speaker to the audience is not disrupted by feedback from your microphone – thank you!

ABSTRACT: Apex predators are making a comeback in many parts of the world. This has sparked global interest in exploring how apex predators interact with other components of the ecosystem. In particular, there is interest in understanding how apex predators interact with lower order competitors or mesopredators. The expectation is that apex predators will suppress the abundance of mesopredators, but there have been few efforts to quantify this phenomenon at large spatial scales.

In this talk, I will outline the results of a new study that assessed whether apex predators can suppress the abundance of mesopredators at large spatial scales. I will outline the implications of the study for conservation, focusing broadly on the global extinction crisis.

In doing so, I will show that direct killing of wildlife by humans remains one of the greatest threats to the persistence of many species, that there is an urgent need to study the ecological role of apex predators in human dominated landscapes, and that we need to shift our conservation efforts to the smaller species who are just as threatened as the largest.

BIO: Thomas Newsome is an Alfred Deakin Postdoctoral Research Fellow and former Fulbright Scholar. He has broad research interests in the ecology, conservation and management of mammals.

His research addresses how species respond to human-induced changes to the landscape. He is particularly interested in how humans and top predators shape and drive ecosystem processes.

Appointments with guest speaker may be made via Euan Ritchie.

CIE Spotlight: Cost and feasibility of a barrier to halt the spread of invasive cane toads in arid Australia: incorporating expert knowledge into model-based decision-making

Emily N.

Authors: Darren Southwell, Reid Tingley, Michael Bode, Emily Nicholson, Ben L. Phillips

Source: JOURNAL OF APPLIED ECOLOGY, 54 (1):216-224, FEB 2017

Brief summary of the paper: Active engagement with practitioners is a crucial component of model-based decision-making in conservation management; it can assist with data acquisition, improve models and help narrow the ‘knowing–doing’ gap.

We worked with practitioners of one of the worst invasive species in Australia, the cane toad Rhinella marina, to revise a model that estimates the effectiveness of landscape barriers to contain spread. The original model predicted that the invasion could be contained by managing artificial watering points on pastoral properties, but was initially met with scepticism by practitioners, in part due to a lack of engagement during model development.

We held a workshop with practitioners and experts in cane toad biology. Using structured decision-making, we elicited concerns about the original model, revised its structure, updated relevant input data, added an economic component and found the most cost-effective location for a barrier across a range of fixed budgets and management scenarios. We then conducted scenario analyses to test the sensitivity of management decisions to model revisions.

We found that toad spread could be contained for all of the scenarios tested. Our modelling suggests a barrier could cost $4·5 M (2015 AUD) over 50 years for the most likely landscape scenario. The incorporation of practitioner knowledge into the model was crucial. As well as improving engagement, when we incorporated practitioner concerns (particularly regarding the effects of irrigation and dwellings on toad spread), we found a different location for the optimal barrier compared to a previously published study (Tingley et al. 2013).

Synthesis and applications: Through engagement with practitioners, we turned an academic modelling exercise into a decision-support tool that integrated local information, and considered more realistic scenarios and constraints. Active engagement with practitioners led to productive revisions of a model that estimates the effectiveness of a landscape barrier to contain spread of the invasive cane toad R. marina. Benefits also include greater confidence in model predictions, improving our assessment of the cost and feasibility of containing the spread of toads.


CIE Spotlight: Seed germination in a southern Australian temperate seagrass

Erin C., Craig S., Paul Y. and Timothy S.

Authors: Erin Cumming​, Jessie C. Jarvis, Craig D.H. Sherman, Paul H. York, Timothy M. Smith

Source: PeerJ, 23 March 2017

Brief summary of the paper: In a series of experiments, seeds from a temperate seagrass species, Zostera nigricaulis collected in Port Phillip Bay, Victoria, Australia were exposed to a range of salinities (20 PSU pulse/no pulse, 25 PSU, 30 PSU, 35 PSU), temperatures (13 °C, 17 °C, 22 °C), burial depths (0 cm, 1 cm, 2 cm) and site specific sediment characteristics (fine, medium, coarse) to quantify their impacts on germination rate and maximum overall germination.

In southern Australia the seagrass Z. nigricaulis is a common subtidal species; however, little is known about the factors that affect seed germination which is a potential limiting factor in meadow resilience to natural and anthropogenic disturbances.

Overall seed germination was low (<20%) with germination decreasing to <10% when seeds were placed in the sediment. When germination of Z. nigricaulis seeds was observed, it was enhanced (greater overall germination and shorter time to germination) when seeds were exposed to a 20 PSU pulse for 24 h, maintained at salinity of 25 PSU, temperatures <13 °C, in sediments with fine or medium grain sand and buried at a depth of <1 cm.

These results indicate that germination of Z. nigricaulis seeds under in situ conditions may be seasonally limited by temperatures in southern Australia. Seed germination may be further restricted by salinity as freshwater pulses reaching 20 PSU are typically only observed in Port Phillip Bay following large scale rainfall events.

As a result, these populations may be particularly susceptible to disturbance with only a seasonally limited capacity for recovery.

Prof. Marcel Klaassen hands the reigns as CIE Director to Prof. Don Driscoll

Marcel K.

We would like to take this opportunity to thank Prof. Marcel Klaassen for being with the CIE from day one and to acknowledge his outstanding contribution to the Centre since then. Marcel served as Director of CIE since 2010 and worked day and night to place the centre as one of Deakin’s leading strategic research centers. He will continue to be part of the CIE as a member of the board and will continue his research work.

Don D.

Prof. Don Driscoll is taking over as the new Director of CIE. Don has a very broad interest in ecological research and a strong track record in leading people and organisations (he is also the President @ Ecological Society of Australia).

On behalf of everyone in the CIE we would like to wish Don all the best!

CIE Spotlight: Fragmentation affects plant community composition over time

Don D.

Authors: C. D. Collins, C. Banks-Leite, L. A. Brudvig, B. L. Foster, W. M. Cook, E. I. Damschen, A. Andrade,M. Austin, J. L. Camargo, D. A. Driscoll, R. D. Holt, W. F. Laurance, A. O. Nicholls, J. L. Orrock

SourceECOGRAPHY, 40 (1):119-130, JAN 2017

Brief summary of the paper:  Habitat fragmentation can lead to major changes in community composition, but little is known about the dynamics of these changes, or how community trajectories are affected by the initial state of habitat maturity.

We use four landscape-scale experiments from different biogeographic regions to understand how plant community composition responds to fragmentation over decades. Within each experiment, we consider first whether plant communities in the most-fragmented treatments diverge in composition from plant communities in the least-fragmented treatments.

Second, because communities embedded in different fragments may become more similar to one another over time (biotic homogenization), we asked whether beta diversity – compositional variation across space – declines among fragments over time.

Third, we assessed whether fragmentation alters the degree to which temporal change in fragmented landscapes is due to ordered species losses and gains (nestedness) versus species replacements (turnover).

For each of these three questions, we contrasted patterns of compositional change in mature communities following fragmentation (disassembly; n = 2 experiments) with patterns in newly-developing plant communities in fragments cleared of vegetation (assembly; n = 2 experiments).

In the two studies where communities were disassembling, community composition in the most-fragmented habitats diverged from that in least-fragmented habitats. Beta diversity within a fragmentation treatment did not change over time at any of the four sites. In all four experiments, temporal patterns of compositional change were due mostly to species turnover, although nestedness played a role in the least-fragmented sites in two of the studies.

Overall, the impacts on community composition varied among landscape experiments, and divergence may have been affected by the maturity of the plant community. Future comparisons across ecosystems that account for species identities (vs simply richness) will be critical for predicting the effects of fragmentation, managing mature plant communities in remnants, and restoring plant communities where habitat has been lost.

CIE Seminar Series 2017 – Functional annotation of avian genomes and the emergence of avian phylogenomics

SPEAKER: Prof David Burt, Department of Genomics and Genetics, The Roslin Institute and Royal School of Veterinary Studies, University of Edinburgh

DATE: Friday, 21st April 2017
LOCATION: Geelong Campus at Waurn Ponds – room ka4.207
TIME: 1:30pm
Seminar will also be video linked to the following campuses: Melbourne Campus at Burwood – Burwood Corporate Centre (attendees-please report to reception on the day); and Warrnambool Campus – room B3.03

External visitors – wish to join us and connect to our seminars?

  • You may connect to the live seminar via *N SEBE VMP LES Seminars [ID.36958] or via the methods listed HERE.
  • For Deakin staff and students, please join via Skype for Business (Lync).
  • Could not log in? More info on how to connect is available HERE.
  • Please note that connection is only available while a seminar is taking place.

As a courtesy, we request that when connecting to the seminar that you mute your microphone unless you are required to speak, this would ensure that the sound from the speaker to the audience is not disrupted by feedback from your microphone – thank you!

ABSTRACT: Our knowledge of avian genomes has increased rapidly, starting with the publication of the chicken genome in 2004, a milestone for avian and evolutionary biology. Advances in DNA sequencing now make it possible to produce draft sequences of any vertebrate genome, quickly and cheaply. We have seen the completion of draft genomes of more than 50 other birds, with plans to sequence all 10,000 by the B10K Consortium.

With advances in long read sequencing and optical mapping, we are seeing chromosome level genome assemblies with N50 contigs of 20-30Mb.  The annotation of genomes has also been under continuous improvement, taking advantage of transcriptome data generated both by short and long read RNA sequencing technologies.

Recently, we sequenced normalised full-length chicken cDNA libraries with Pacific Bioscience Iso-Seq. From these Iso-Seq sequencing projects, over 60K transcripts and 29K genes were defined within the chicken transcriptome. Of these, more than 20K are novel long non-coding RNA (lncRNA) transcripts with approx. 3K classified as sense-exonic overlapping lncRNA, which is a class that is underrepresented in all other vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes.

Our results indicate that the chicken transcriptome is similar in complexity (with multiple starts and stops, and alternative isoforms) compared to human. Our improved methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of the transcriptomes of any complex organism. Recently, the analysis of 44 bird genomes by the Avian Phylogenomics Consortium created new opportunities. For individual species, the sequences coupled with the initial annotations, can serve as a vehicle for basic research. On the other hand generating a multiple genome sequence alignment can enable comparative studies, which benefits all these species. Such studies broaden our understanding of genome evolution and the evolution of traits or can help to disentangle phylogenetic relationships.

Our main aim is to integrate these and other data sources (transcripts, CAGE-seq, ChIP-seq, ATAC-seq, etc. for example as part of the FAANG initiative) with a focus on creating a detailed functional map relevant to birds. Such a map can be used to drive the identification of novel protein-coding and non-coding genes, binding sites for transcription factors, enhancers or other functional elements.

I will review the current status of avian genome annotation and open up the discussion on future possibilities using phylogenomics in the study of species diversity and the evolution of avian traits.

BIOProfessor David W. Burt, FRSB, FLS received his B.Sc. in Molecular Biology at Edinburgh University (1977), a PhD in molecular genetics from Leicester University (1980) and MSc modules in Bioinformatics from Manchester University (2002). His post-doctoral training included research on molecular genetics of a wide range of species (bacteriophage lambda, bacteria, mouse, rat and human) and research areas (transcription circuits, cDNA cloning of growth factors, renin-angiotensin system and hypertension, QTL mapping, bioinformatics, phylogenetics and avian genomics). He has worked with AstraZeneca at Leicester University (UK), Harvard Medical School (USA), MRC Clinical Research Centre (UK) and Roslin Institute/Edinburgh University (UK). He was appointed Head of Avian Genomics Group (1988), Director of ARK-Genomics (2000), Director of the National Avian Research Facility (2014), convener of Institute Strategic Program (Genomics, 2016) and Personal Chair in Comparative Genomics, University of Edinburgh (2009).

In 2017, Professor David W. Burt was appointed Director of the UQ Genomics Initiative  a virtual network that aims to facilitate partnerships and engagement across all genomics researchers at UQ and beyond. UQ genomics research has the potential for strong synergies with The Roslin Institute and we hope to develop this relationship over the coming years. To facilitate this Professor Burt will continue to work closely with The Roslin Institute in his new capacity at UQ and will hold an honorary Chair in Comparative Genomics at Edinburgh University.

He has obtained over $70m in competitive funding to support his research activities and has published over 300 articles, books and chapters (h-index 57) including in high impact journals such as Nature, Science, Nature Genetics, Current Biology and Genome Research. His current research is focused on comparative genomics and applications in poultry and other livestock species.  He has served on many scientific committees, including the BBSRC Animal Science Committee, the Scottish Branch Council of the Royal Society of Biology, the Board for Edinburgh Genomics and several editorial boards. He is active in promoting avian genomics as co-chair in various consortia and international meetings, including the International Chicken Genome Consortium, International Society for Animal Genetics (ISAG), Bird10K, Avian Model Systems, Plant & Animal Genome workshop on Avian Genomes and theInternational Functional Annotation of Animal Genomes (FAANG) Steering Committee.

The UQ Genomics Initiative offers a clear point of entry to UQ’s collective genomic capabilities, including its interactions with government and industry. The Director ensures that the UQ Genomics Initiative facilitates interdisciplinary interactions in fundamental and applied research, education, training and consulting across all faculties and institutes. It is my goal to build synergies throughout Australasia to promote and enhance a regional Genomics Community.

Appointments with guest speaker may be made via Kate Buchanan.

CIE Spotlight: Navigating uncertainty in environmental composite indicators

Emily N.

Authors: Michael J. Burgass, Benjamin S. Halpern, Emily Nicholson, E.J. Milner-Gulland

Source: Ecological Indicators, Volume 75, Pages 268–278, April 2017

Brief summary of the paper: Composite indicators (CIs) are increasingly used to measure and track environmental systems. However, they have faced criticism for not accounting for uncertainties and their often arbitrary nature.

This review highlights methodological challenges and uncertainties involved in creating CIs and provides advice on how to improve future CI development in practice. Linguistic and epistemic uncertainties enter CIs at different stages of development and may be amplified or reduced based on subjective decisions during construction. Lack of transparency about why decisions were made can risk impeding proper review and iterative development. R

esearch on uncertainty in CIs currently focuses on how different construction decisions affect the overall results and is explored using sensitivity and uncertainty analysis. Much less attention is given to uncertainties arising from the theoretical framework underpinning the CI, and the sub-indicator selection process. This often lacks systematic rigour, repeatability and clarity.

We recommend use of systems modelling as well as systematic elicitation and engagement during CI development in order to address these issues. Composite indicators make trends in complex environmental systems accessible to wider stakeholder groups, including policy makers. Without proper discussion and exposure of uncertainty, however, they risk misleading their users through false certainty or misleading interpretations.

This review offers guidance for future environmental CI construction and users of existing CIs, hence supporting their iterative development and effective use in policy-making.

CIE Spotlight: Genetic and morphological analyses indicate that the Australian endemic scorpion Urodacus yaschenkoi (Scorpiones: Urodacidae) is a species complex

Adam M.

Authors: Karen Luna-Ramirez, Adam D. Miller, Gordana Rašić

Source: PEERJ, 5, JAN 2017

Brief summary of the paper:

Background: Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones of the continent and is emerging as a model organism in biomedical research due to the chemical nature of its venom.

Methods: We employed Bayesian Inference (BI) methods for the phylogenetic reconstructions and divergence dating among lineages, using unique haplotype sequences from two mitochondrial loci (COXI, 16S) and one nuclear locus (28S). We also implemented two DNA taxonomy approaches (GMYC and PTP/dPTP) to evaluate the presence of cryptic species. Linear Discriminant Analysis was used to test whether the linear combination of 21 variables (ratios of morphological measurements) can predict individual’s membership to a putative species.

Results: Genetic and morphological data suggest that U. yaschenkoi is a species complex. High statistical support for the monophyly of several divergent lineages was found both at the mitochondrial loci and at a nuclear locus. The extent of mitochondrial divergence between these lineages exceeds estimates of interspecific divergence reported for other scorpion groups. The GMYC model and the PTP/bPTP approach identified major lineages and several sub-lineages as putative species. Ratios of several traits that approximate body shape had a strong predictive power (83–100%) in discriminating two major molecular lineages. A time-calibrated phylogeny dates the early divergence at the onset of continental-wide aridification in late Miocene and Pliocene, with finer-scale phylogeographic patterns emerging during the Pleistocene. This structuring dynamics is congruent with the diversification history of other fauna of the Australian arid zones.

Discussion:Our results indicate that the taxonomic status of U. yaschenkoi requires revision, and we provide recommendations for such future efforts. A complex evolutionary history and extensive diversity highlights the importance of conserving U. yaschenkoi populations from different Australian arid zones in order to preserve patterns of endemism and evolutionary potential.

Dr Lucie Bland – 2017 Finalist @ The Victorian Young Achiever Awards

Congratulations to Dr Lucie Bland for being a finalist for the Victorian Young Achiever Awards (Research Impact Award).

The purpose of the Victorian Young Achiever Awards is to acknowledge, encourage and most importantly promote the positive achievements of all young people up to and including 29 years of age as of 31st December each year.

For more information about the Victorian Young Achiever Awards and full list of VIC 2017 finalists CLICK HERE.