Forensic Genomics of the Illicit Parrot Trade in Indonesia

Southeast Asia is both a major hotspot for biodiversity and is also the epicentre for illegal wildlife trade world-wide. Among CITES listed species, parrots are by far the most traded. Our comprehensive evaluation of the global status of parrots revealed that one-third of the nearly 400 species are threatened by extinction, and that parrots decline faster than any other comparable bird group. The unsustainable parrot trade together with habitat destruction are one of the major causes of their rarity. In our recent study (Olah et al. 2018, Emu), Indonesia was flagged as the highest priority country for parrot conservation, reflecting many threatening factors: high species diversity (many endemics), large and forest dependent species (like cockatoos), large human population and areas of agriculture (mainly monocultures). We also showed that the negative effects of wildlife trade are already measurable on the wild parrot populations in a biodiverse Indonesian island (Nandika et al. 2021, Diversity).

This project is developing cutting-edge, field-based genomic techniques for solving wildlife trade issues in a biodiversity hotspot. Such molecular genomic methods are widely applied to provide forensic evidence for litigation, including the illegal hunting and collection. The research will achieve important, pro-active countermeasures with practical outcomes to the local and international wildlife trade, and applicability world-wide. This multidisciplinary project draws on genomics and criminology to combat the illegal trade and restore threatened populations, while increasing local and international awareness of the impact.

This project is funded by the Australian Research Council, under a Discovery Early Career Researcher Award (DECRA project DE230100085), and hosted by the Fenner School of Environment and Society, The Australian National University (ANU). Our Indonesian collaborators are Prof. Dewi Prawiradilaga (BRIN) and the Konservasi Kakatua Indonesia. My international collaborators for this research include the Indonesian Parrot Project, Prof. Sam Banks (Charles Darwin University), Prof. Denise Syndercombe Court (King’s College London), Dr. Stephen Pires (Florida International University), and Prof. Rob Heinsohn (ANU).

Remote Sensing and Landscape Genetics

In a collaboration with spatial ecologist Prof. Greg Asner (Global Airborne Observatory) and Dr. Anabel Smith (University of Queensland), we combined their remotely sensed data with my population genetic information on Red-and-green Macaws, revealing differences between the studied macaw populations and related their genetic structure to landscape features. Our publication (Olah et al. 2017, Landscape Ecology) provided baseline landscape genetic information about natural dispersal barriers in macaws that can assist in understanding the influence of rapid anthropogenic change on their genetic population structure in the Amazon Basin.

In our ongoing collaboration with Dr. Asner as the director of the Center for Global Discovery and Conservation Science (Arizona State University), we are investigating if forest functional diversity can explain threats to bird populations and communities by using the world’s first functional biodiversity map of the entire area of Peru. Many birds depend on forests, so functional diversity in these habitats might translate to functional diversity in specific bird groups. If these relationships are defined, remote sensing can aid in functional biodiversity monitoring and assigning priority areas for conservation.

I collaborated with Biogeographer Dr. Javier Nori and his team at the Centro de Zoología Aplicada (Universidad Nacional de Córdoba) and the Instituto de Diversidad y Ecología Animal (CONICET-UNC) in Argentina. In our study we investigated the current and predicted effects of forest habitat destruction on the conservation status of parrots worldwide (Vergara-Tabares et al. 2020, Global Change Biology). We highlighted, that the current extent and locations of the protected areas are insufficient in safeguarding most of these threatened species.

Ancient Feather DNA Study

In collaboration with Anthropologist Prof. Izumi Shimada (Southern Illinois University, USA) we collected parrot feathers from a pre-Hispanic archaeological site in the Atacama Desert of Peru. As parrots do not occur naturally in that region, we were interested in their provenance. Colleagues at the Australian Centre for Ancient DNA (ACAD) successfully extracted and sequenced ancient DNA (aDNA) from the ancient feather tissues found in the burial sites. Currently, we are analysing the results with Dr. Pere Bover (Universidad de Zaragoza, Spain) to identify the species and the possible geographic origin of the feathers.

Difficult Bird Research Group

The Difficult Bird Research Group (DBRG) of Prof. Robert Heinsohn studies Australia’s most endangered birds and is dedicated to understanding their ecology and conservation. Their research focuses on understanding the processes that threaten endangered birds, and identifying the ways to prevent extinction. The ‘difficult birds’ are all extremely endangered, hard to find, occur in wild and rugged terrain, and move around the landscape.

I was employed as a Postdoctoral Research Fellow at the Fenner School of Environment & Society, ANU, dedicated to full-time research. The DBRG has accumulated hundreds of genetic samples from the Critically Endangered Swift Parrot (Lathamus discolor) of Tasmania over the years. I processed these samples and analysed the genetics of this iconic Australian species. The results of these analyses have provided important management information for their conservation, implemented in the field. With my research group I have published three papers from this study: the first presented genetic evidence confirming the severe extinction risk of this species (Stojanovic et al. 2018, Animal Conservation), the second showed how sex ratio bias and shared paternity reduce their population viability (Heinsohn et al. 2019, Journal of Animal Ecology), and a third presenting techniques to estimate the effective population size in endangered species (Olah et al. 2020, Animal Conservation).

During my postdoc I won the prestigious Endeavour Postdoctoral Research Award. During this research position I was interested in population genetic changes of the Critically Endangered Regent Honeyeater (Anthochaera phrygia) through space and time, and in estimating the population size over a 100-year time frame, using mainly museum samples. Museum collections are becoming increasingly important in conservation genomic studies as they are repositories of genetic materials from the past. We collected genetic samples from the remaining populations of this species, and also collaborated with many national and international museums to investigate the magnitude of the genetic diversity lost in these birds. In close collaboration with the Banks, Peakall, and Moritz labs, I adjusted the existing genomics protocols to work with both ancient (aDNA) and modern DNA samples. I eventually applied next-generation sequencing (NGS) technology: a hybridization RAD technique that included ddRAD library preparation of the probes from contemporary samples, in order to hybridize with fragmented aDNA successfully extracted from museum specimens (Olah et al. 2018, Our results showed that the population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range (Crates et al. 2019, PLOS ONE).

Ecology and Population Genetics of Two Large Macaw Species in the Peruvian Amazon

My PhD project was completed at The Australian National University (ANU) through a prestigious international scholarship (IPRS) from the ANU and an Endeavour Scholarship from the Department of Education of the Australian Government. My research focused on the ecology and conservation of wild macaw populations in the Peruvian Amazon. As part of this research I gained extensive experience in the nesting ecology of wild parrots and in genetics. As presented in a series of my publications, I developed and validated non-invasive DNA collection methods for the first time on wild birds in tropical settings to reconstruct their population genetic structure. I used population genetic modelling to reveal differences among the studied macaw populations, and to relate the genetic structure of the populations to landscape features. I published all seven chapters of my PhD research.

The order Psittaciformes (parrots) contains 398 extant species, divided into 3 families (Psittacidae 374, Cacatuidae 21, Strigopidae 3 species) of which 111 (28%) are classified as threatened on the IUCN Red List. My PhD research presented a wide array of interdisciplinary methods to study parrots: statistical modelling of their extinction risk, on site ecological studies of nest preferences, and population genetic techniques.

I modelled the factors associated with extinction risk in parrots, including intrinsic biological, life history and ecological attributes, external anthropogenic threats, and socio-economic variables of the countries where they occur (Olah et al. 2016, Biodiversity and Conservation). I found a range of significant effects on parrot conservation status including historical distribution size, forest dependency, body size, generation time, the proportion of the human population living in urban areas in the countries encompassing the parrots’ home ranges, per capita GDP of the countries of occurrence, endemism to a single country, and whether the species are used as pets.

Most parrots are obligate secondary cavity nesters, and can be limited in their breeding success by the availability and quality of nest hollows. I evaluated how nesting opportunities for parrots can be increased by provision of artificial nest boxes (Olah et al. 2014, Journal for Nature Conservation). My results show that artificial nests can be used by conservation managers seeking to assist macaw populations where nest hollows are in short supply, and that artificial nests can contribute important data to natural history studies of species where access to natural nests is limited. I showed that Philornis sp. bot fly larvae prevalence was higher in artificial nests than in natural nests. I also described a new field technique of removing Philornis larvae using a snakebite extractor pump (Olah et al. 2013, Veterinary Parasitology).

While extended knowledge about the natural history and ecology of species is crucial for their conservation, by combining ecology and genetics we can reveal new insights not evident from either ecology or genetic studies alone. I developed species-specific microsatellite (STR) genetic markers for scarlet macaw (Ara macao) based on their full genome (Olah et al. 2015, Conservation Genetics Resources). Using these new genetic markers I validated their potential for genetic tagging by using blood samples and moulted feathers of two sympatric macaw species in the Peruvian Amazon (Olah et al. 2016, Conservation Genetics Resources).

I applied non-invasive genetic tagging technique to estimate population size of red-and-green macaws (Ara chloropterus) in the Tambopata region of southeastern Peru (Olah et al. 2017, Conservation Genetics). These conservation genetics techniques can be implemented for other related species with higher conservation concern, while also determining population structure and measuring levels of genetic diversity.

Landscape genetics provide an extra framework to study population dynamics, revealing the landscape factors that contributed to the genetic structure. I used landscape genetic resistance models to confirm isolation by elevation due to the mountain ridges between macaw populations in Candamo (an intermountain valley) and the lowland rainforest of Tambopata (Olah et al. 2017, Landscape Ecology). Maintaining large protected areas and giving conservation priorities for intermountain rainforest valleys are essential for conserving the current genetic diversity of scarlet macaws in Peru.

The following supporters made my PhD project possible: