Pacific Rim nations harbour a substantial proportion of the Earth’s nine million species, including several biodiversity hotspots. Genome analysis is now recognised as a fundamental tool in understanding this incredible biodiversity and assisting with its preservation. Although genome sequencing at scale is becoming more affordable, significant challenges remain in achieving the goal of sequencing all known species and deriving useful biological information from these data.
The symposium marks the launch of the Association of Pacific Rim Universities (APRU) Biodiversity Program, which seeks to enhance cooperation and synergies among its members in the field of biodiversity and related sciences. This inaugural event brings together leading genomics experts from Pacific Rim nations to discuss progress in this area, the challenges they face, and how collective action can advance biodiversity genomics in the region.
This webinar will be beneficial to academics and industry partners, we welcome the participation of all students and staff alike.
Date & Time
November 29 at 4 pm (PST)/ 7 pm (Bogota)
November 30 at 7 am (Bangkok & Jakarta)/ 8 am (Hong Kong & Manila)/ 11 am (AEDT)
See a time converter here.
Duration 2 hours
Prof. Harris Lewin, University of California, Davis
The Earth BioGenome Project: Science at the Nexus of the Global Biodiversity and Climate Crises
Speaker Prof Harris A. Lewin is the Robert and Rosabel Osborne Endowed Chair and Distinguished Professor of Evolution and Ecology and at the University of California, Davis where he also holds joint appointments in the School of Veterinary Medicine and the John Muir Institute for the Environment. From 2011-2016, he served as the UC Davis Vice Chancellor for Research. Prior to that he spent 27 years at the University of Illinois at Urbana-Champaign, where he held the E.W. and J.M. Gutgsell Endowed Professorship in Immunogenetics, with a primary appointment in the Department of Animal Sciences and was a member of the Center for Advanced Study. Lewin served as Director of the University of Illinois Biotechnology Center, Founding Director of the W.M. Keck Center for Comparative and Functional Genomics, and Founding Director of the Institute for Genomic Biology. Lewin’s current research interest is in mammalian genome evolution as it relates to adaptation, speciation, and the origins of cancer. In 2017, Lewin co-founded the Earth BioGenome Project (EBP) and currently serves as the Chair of the EBP Working Group. He is a Fellow of the American Association for the Advancement of Science, and was elected as a foreign member of the Royal Swedish Academy of Agriculture and Forestry. In 2011, Lewin was awarded the Wolf Prize in Agriculture, and in 2013 he was elected to the U.S. National Academy of Sciences.
Earth is in the midst of a global biodiversity crisis, with species disappearing at over 1,000 times the natural extinction rate. Extinction is irreversible, eradicating genetic diversity that has taken millions of years to evolve. This so-called 6th Mass Extinction threatens vital ecosystems on which humans depend. It may not be possible to slow or halt biodiversity loss without a deeper understanding of the origins, evolution, adaptability, and ecological functions of diverse species. In addition, the rapidly growing worldwide bioeconomy and emerging needs in pandemic responsiveness require broadening our understanding of life’s biodiversity. The Earth BioGenome Project (EBP) aims to sequence, catalog, and characterize the genomes of all of Earth’s plant, animal, and other eukaryotic biodiversity. The ultimate aim is to use these genomes as a foundation for revealing the “rules of life,” i.e., how biological complexity arose, the relationship between genotype and phenotype, and how biological systems evolve under changing environmental conditions. Accomplishing these goals requires coordination of interdisciplinary coordination at a global scale. I will discuss the organization and strategy employed by the EBP, as well as early progress and the critical challenges ahead.
Biodiversity genomics in Colombia, South America: challenges and solutions.
Speaker Andrew J. Crawford received his PhD in Evolutionary Biology from the University of Chicago with Marty Kreitman after completing a dual undergraduate degree in Zoology & German at UC Berkeley with David Wake in the Museum of Vertebrate Zoology. He then joined the Smithsonian Tropical Research Institute in Panama as an NSF International Programs Postdoctoral Fellow followed by a Smithsonian Postdoctoral Fellowship in Molecular Evolution with Biff Bermingham. In 2009 he became a Professor of Biology at the Universidad de los Andes in Bogotá, Colombia, where he is currently Associate Professor and Director of the Museo de Historía Natural C.J. Marinkelle. Andrew is Executive Council member of the Vertebrate Genomes Project (VGP) and representative of the Earth BioGenome Project (EBP) Colombia. His laboratory explores the origins, adaptations, and conservation of amphibians and other vertebrates in Tropical America using genetics, genomics, physiology, spatial analyses, and natural history collections.
Biodiversity sustains human life and can drive a sustainable green economy. Because the foundational unit of biological diversity is the nucleotide, understanding genome sequence variation and function is becoming a critical component of biodiversity sciences. Global biodiversity is concentrated in tropical regions, while genome sequencing technology and resources are concentrated at higher latitudes and this asymmetry has created challenges for biodiversity genomics. Colombia is a megadiverse country still developing social security and economic prosperity. Biodiversity genomicists have formed ‘EPB Colombia’, an important node in the Earth BioGenome Project, and engaged with the government to recognize the nation’s rich biodiversity as its greatest resource and an engine for driving a sustainable bioeconomy. This talk will review biodiversity genomics in Colombia and current initiatives. We will highlight sequencing and assembly strategies used so far, address diverse challenges, and discuss past and future solutions. While the challenges are multifaceted, and the solutions preliminary, EBP Colombia may serve as an example of navigating the asymmetry between megadiverse tropical countries and countries with robust resources and sequencing infrastructure based on a foundation of mutual trust, international regulations, and shared goals.
Australian Biodiversity Genomics
Speaker Dr Carolyn Hogg has been working on the conservation of threatened species for over twenty-five years both in Australia and overseas. She is currently the Senior Research Manager for the Australasian Wildlife Genomics Group in the Faculty of Science at the University of Sydney and the Science Lead for the Threatened Species Initiative, which is generating genomic resources for Australia’s threatened species. Dr Hogg has been working with the Save the Tasmanian Devil Program for the past ten years; in addition to other species such as orange-bellied parrots, koalas, bilbies, and woylies. Working closely with both her academic and conservation management partners Dr Hogg’s vision is to create a conservation legacy for Australia by changing the way we integrate science, management, and policy; to proactively promote species’ resilience in the face of a changing world. She is achieving this by developing better tools and technologies to integrate molecular genetics into real-time conservation management decisions.
The age of genomics is here and has the potential to change the way we manage and conserve global biodiversity. Genomics is a powerful tool which can be used to inform on ground management actions for species protection, advance our knowledge of species biology and taxonomy, and inform policy and decision-making frameworks. Here we present how we are integrating genomics into the conservation of Australian biodiversity highlighting our current challenges and future opportunities.
Indonesian Biodiversity Genomics: Challenges and Opportunity.
Speaker Dr Herawati Sudoyo is the Deputy for Fundamental Research of Eijkman Institute. She is also the head of Forensic DNA Laboratory and Principal Investigator at Genome Diversity and Diseases Laboratory. She specializes on mitochondria DNA as a powerful genetic markers for population studies. She has specific interests on fundamental information concerning the formation of functional mitochondrial in order to understand mitochondrial diseases and its diagnostic and therapeutic implications. Herawati also has big passion on studying the genetic diversity of Indonesian populations, particularly on its association with disease resistance and susceptibility as well as tracing human migration. Her research team is dubbed "Gene Hunter" and has been collecting samples from many places throughout the archipelago, including very remote areas. Using DNA markers, Herawati also played significant role in perpetrator identification of the 2004 Australian Embassy bombing case which subsequently led her to establish the Forensic DNA Laboratory in Eijkman Institute. She also initiates research on Indonesian wildlife forensics and population studies.
Herawati is an active member of various local and international organization, consortium, and scientific panel on forensics DNA, biorisk and biosafety, human genetics, and molecular biology network.
Herawati is an Honorary Associate Professor from Sydney Medical School, The University of Sydney.
Climate change and evolution in the tropics: a genomic perspective
Speaker Balaji Chattopadhyay is an Assistant Professor at the Trivedi School of Biosciences, Ashoka University. He completed his PhD from Madurai Kamaraj University and pursued postdoctoral research at the National Centre for Biological Sciences, India, and the National University of Singapore, Singapore. Balaji is an evolutionary biologist whose research aims to integrate biodiversity conservation and human health. Balaji provided one of the earliest evidence of the susceptibility of natural populations to urbanisation. His research incorporates high-throughput genomic data alongside biological and ecological data to understand the effects of climate change on wildlife and investigate the potential link between wildlife endangerment and zoonotic infections. Balaji is also interested in understanding host-pathogen coevolution, specifically in regards to the evolutionary dynamics of the bat immune system and bat-borne viruses.
The current epoch known as the Anthropocene, is characterized by unprecedented loss of biodiversity and threat to wildlife in general. A thorough understanding of biotic evolution under regimes of climate change is necessary to prevent further extirpation of natural populations and is critical towards developing predictions for species responses to future climatic fluctuations. While many studies have investigated the impact of the Last Glacial Maxima and Holocene on species diversity and demographic history, only recently it has been possible to elucidate the impact of the last century on species diversity. Availability of genomic data from century old museum samples have allowed comparisons of current and historical genetic diversity, thereby facilitating efforts to explore the impact of Anthropocene on the evolution of natural populations. This talk will discuss the application of genomic data to investigate the evolution of natural populations of bats in response to climate change as well as the Anthropocene. In addition, we will also discuss some of the contributions of the SEABIG (Southeast Asian Biodiversity Genomics) initiative into biotic evolution and conservation management.
Advent of Genetics and Genomics paving way to manage the Malaysian biodiversity resources from 2021-2030
Speaker Prof Dr Subha Bhassu is currently Head of Animal Genetics and Genome Evolutionary Biology Lab which is affiliated to Institute of Biological Science, Faculty of Science, University Malaya. In her 25 years of teaching and research in the area of genetics and genomics and use this expertise to address biodiversity problems arise in Malaysia. With use of molecular markers as a tool to address ecological, conservation, management in biodiversity such as addressing the forest species, animal species, aquatic species and insect species. There are many ways to give insights to raise awareness of the public on biodiversity, currently we will use predictive models on assessing the impact of invasive alien species, EDNA metagenomics to access the aquatic biodiversity in freshwater ecosystem to ensure the research will be used by policy makers and attempt to govern the freshwater ecosystem in a sustainable manner in line with SDGs.
The sequencing technology aided with genomics coupled with sound genetics, ecology and biology of species has sparked many researchers in Malaysia to use this technology in addressing the challenges of managing resources and its environment in a sustainable manner. The collaboration between Universities, Research institutions, Industry and NGOs have attempted to work in managing the biodiversity and resources and this will be presented as successful case studies of last 10 years. Currently, no doubt, we face challenge on justification of new projects that needs comprehensive insights with sampling, sequencing, computation and bioinformatics and inadequate young talents that move to other fields due to problems in jobs related to genomics studies in biodiversity area. Thus, the need is , we would like to provide ideas and solutions by effective collaboration and strategic partnership, we are able to work on addressing using genomics approach in managing biodiversity in our respective countries.
Coconut genomics initiative in the Philippines: updates and opportunities for biodiversity data
integration and further genomics research collaboration
Speaker Dr Hayde F. Galvez is an Assistant Professor, Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños. Completed PhD in Molecular Genetics and Plant Breeding from the University of Melbourne, Australia. Other significant work experiences included Fulbright Advance Research Fellow on Bioinformatics at the Boyce Thompson Institute for Plant Research, Cornell University, USA; Molecular Marker Specialist at AVRDC – The World Vegetable Center, Taiwan; and as a Junior Plant Breeder at East West Seed Co. Inc. She has completed and on-going research projects on crop molecular genetics, breeding, genomics and agricultural biotechnology. Example was her program and project leadership in a 5-year Coconut Genomics Program consisted of eight component research projects. Publications of research outputs are presented on peer-reviewed journals, and in local and international scientific fora/conferences.
The Philippines is the second world supplier of coconut by-products. To support and provide advance genetics tools for the challenging, yet critical for the current times, development of resilient and outstanding varieties especially for added high-value traits, a high quality genome assembly was generated and being used to characterize adaptation and economically important genes. Coconut whole genome sequence (WGS) was assembled using the Philippine ‘Catigan Green Dwarf’ (CATD) variety and combinations of different next generation sequencing (NGS) platforms. A big challenge for the Philippine researchers to work in coconut for its first WGS research project. This was however facilitated with the all-out government support and strong collaboration among multidisciplinary experts and partnership with international leading institute/research group.
Updates including challenges encountered will be presented on the specific applications of the output from the coconut genomics project. These include gene mining for host insect resistance and screening for least damaged coconuts (thus potentially insect resistant varieties), as well as characterization of coconut genes related to coconut oil qualitative/quantitative traits. Significant result from initial molecular and biochemical studies that support nutritional and medicinal claims will also be presented. The unprecedented opportunities for global collaboration beyond basic science from these major S&T achievements, and in integration with applicable new breeding technologies, will be put forward for policy consideration in the continuum of coconut R&D.
Genomes of Cnidarians and Non-Insect Arthropods
Speaker Prof Jerome Hui is currently the Associate Professor at The Chinese University of Hong Kong. He is also the Director of Biology Programme, and members of Cell and Molecular Biology Programme, Environmental Science Programme, and Molecular Biotechnology Programme of the School of Life Sciences. He received his DPhil from the University of Oxford, and postdoctoral training from University of Manchester and University of Oxford. As an evolutionary biologist and zoologist, he has keen research interests on arthropods, cnidarians, invertebrates, cross-kingdom interactions, biotechnology, genomics, molecular ecology, and conservation of biodiversity. Further information can be found at the following webpage: https://www.sls.cuhk.edu.hk/index.php/faculty-and-staff/teaching-staff/26-sls/faculty-and-staff/teaching-staff/105-professor-hui-ho-lam-jerome
The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. On the other hand, the phylum Arthropoda is arguably the most successful group of animals comprising more than 80% of the described living species, including insects, crustaceans (crabs, lobsters, shrimps), chelicerates (spiders, ticks, mites, horseshoe crabs), and myriapods (centipedes, millipedes). In this talk, I will discuss some of the key insights coming from our previous sequencing of some of the cnidarian and non-insect arthropod genomes. In addition, I will also share with the audience the current progress of building biodiversity genome sequencing capacity in Hong Kong, the challenges ahead, and hopefully also the potential ways to move forward.
Prof Nathan Lo is an evolutionary biologist interested in genome evolution, molecular ecology, and phylogenetics of arthropods. He has research programs on the evolution of social behaviour in termites and the symbionts of arthropods. After joining the School of Life and Environmental Sciences at The University of Sydney in 2009, he was an Australian Research Council (ARC) QEII Research Fellow from 2010-2014, and is currently an ARC Future Fellow (2017-2021). He was Biodiversity Research Initiative Leader at the Australian Museum, Sydney from 2008-2009. He has published over 140 scientific papers, which have been cited over 8500 times.
Prof Jerome Hui is currently the Associate Professor at The Chinese University of Hong Kong. He is also the Director of Biology Programme, and members of Cell and Molecular Biology Programme, Environmental Science Programme, and Molecular Biotechnology Programme of the School of Life Sciences. He received his DPhil from the University of Oxford, and postdoctoral training from University of Manchester and University of Oxford. As an evolutionary biologist and zoologist, he has keen research interests on arthropods, cnidarians, invertebrates, cross-kingdom interactions, biotechnology, genomics, molecular ecology, and conservation of biodiversity. Further information can be found at the following webpage: https://www.sls.cuhk.edu.hk/index.php/faculty-and-staff/teaching-staff/26-sls/faculty-and-staff/teaching-staff/105-professor-hui-ho-lam-jerome