From clones to conservation: ASU leads global effort to decode whiptail lizard genomes

On June 26, 2000, President Bill Clinton stood at a White House podium announcing the completion of the first draft of the human genome DNA sequence. This was the result of the world’s largest collaborative biological project at that time, the Human Genome Project, with researchers from 20 universities across the U.S., U.K., Japan, China, Germany and France. Advances in the treatment of genetic diseases, personalized medicine, understanding human evolutionary history and forensic science are just a few outcomes of sequencing that first “reference” human genome and the thousands of others that have followed.

The completion of the Human Genome Project also sparked a cascade of collaborative sequencing projects in the genomics field for species across the tree of life, leading to consortiums targeting hundreds to thousands of plant and animal species. In time, this led to the keystone initiative uniting consortiums around the world — the Earth BioGenome Project, or EBP.

The EBP is poised to sequence all 1.8 million currently recognized eukaryotic species (organisms whose DNA is enclosed in a membrane within a cell, such as plants, animals and fungi, as opposed to bacteria, which do not have a cell nucleus). The project is an international coalition of 58 sequencing projects that includes several of the same institutions that led the Human Genome Project. In December 2023, the EBP Secretariat and Harris Lewin, the EBP co-founder and Executive Council Chair, were recruited by ASU’s Julie Ann Wrigley Global Futures Laboratory to expand infrastructure for the EBP’s goal of generating freely available reference-level genomes for all eukaryotes within the next decade.

With ASU now a global center of the EBP, researchers at ASU are embarking on a pilot project focused on genome evolution in a fascinating group of lizard species native to the southwestern United States.

Given the importance of understanding how biodiversity may be affected by changes in climate and the shrinking of natural habitats, the desert Southwest offers an unprecedented opportunity for ASU to contribute to the goals of the EBP and address the critical needs of conservation for future generations of the peoples inhabiting this region.” Lewin says.

North American whiptail lizards (of the genus Aspidoscelis) are composed of 42 species occupying habitats ranging from rainforest edges in southern Mexico to rocky slopes of Arizona’s Superstition Wilderness.

Named for their long, thin, whip-like tails, they are active, fast-moving lizards in which all-female (unisexual) species that reproduce asexually (without fertilization of egg cells) have repeatedly evolved. The offspring of the unisexual (or parthenogenetic) Aspidoscelis species are full clones of their mothers. Due to the unisexual whiptail species being the result of hybridization between two divergent, sexual species, generating a reference genome for each lineage will give scientists the full context of the evolutionary history and sequence-level changes that led to such a unique group of animals.

The project is a collaborative effort between EBP members Harris Lewin, Melissa Wilson, Nate Upham, Postdoctoral Scholar Simone Gable and ASU Assistant Professor Anthony Barley. Barley is an expert on these species with more than 15 years of research experience studying whiptail biology

This summer, researchers will travel to sites throughout Arizona, New Mexico and Central America to collect samples for generating high-quality reference genomes for all whiptail lineages.

The outcomes of this research will answer fundamental questions on the relationship between modes of reproduction, genome evolution and biodiversity. Parthenogenesis can be advantageous in the short term because it lets asexual populations reproduce quickly and spread to new areas without needing a mate. But the lack of meiotic recombination (the genetic mixing prior to egg and sperm production) and the observation that all known asexually reproducing vertebrate species arose relatively recently may suggest that sexual reproduction has bigger advantages over the long term. However, the idea that vertebrate parthenogenesis is an “evolutionary dead-end” is being challenged. This research will help identify if these species have mechanisms that allow them to counter the disadvantages of asexual reproduction, or if their genomes decay over time through the accumulation of mutations because of it.

In the 2016 development paper by Aracely A. Newton and colleagues, researchers found both sexually reproducing and asexual whiptail species have similar levels of reproductive success. Learning how parthenogenesis affects adaptability and genetic diversity can help conservationists tackle the current biodiversity crisis. For example, species listed as threatened or endangered are overrepresented in parthenogenesis reports.

In part, this is because scientists have learned in recent years that many species that were thought to reproduce exclusively using sex, also produce offspring through parthenogenesis at low levels (including primarily sexual whiptail lizards),” says Barley.

He explains that advancing understanding of the mechanisms and consequences of asexual reproduction enables biologists to better account for reproductive mode variation in conservation planning. This opens doors to developing technologies that support the recovery of endangered species and the reduction of pressure on natural ecosystems.

The study of genome evolution and reproduction in whiptail lizards represents a pivotal step in understanding biodiversity and advancing conservation efforts. With the EBP’s ambitious goal of sequencing all eukaryotic life, the collaborative efforts at ASU and beyond are laying the groundwork for transformative discoveries. Unraveling the genetic intricacies not only deepens our understanding of life’s diversity but also holds promise for addressing the global biodiversity crisis, offering innovative solutions to protect endangered species and ecosystems.