Edward David Penny (David), who died on 20 May 2024 at the age of 85, was one of the principal architects of the field of molecular phylogenetics, and drove progress in theory, method development and the reconstruction of evolutionary trees across the tree of life. He pioneered a formal test for the theory of evolution, which demonstrated its falsifiability — something that Karl Popper initially doubted was possible. David worked on major evolutionary questions, from the makeup of the RNA world, the nature of the last universal common ancestor of life, and the origins of the genetic code and the eukaryote cell, to plant and vertebrate diversification and human migrations. He also had a rare ability to get biologists and mathematicians, theoreticians and experimentalists to work together productively. David leaves a theoretical and empirical legacy of staggering breadth.

David was born in 1938 in Taumarunui, New Zealand, and grew up with two siblings. In 1942, his father died in a farm accident and his mother, who had been a teacher, started selling vegetables and cleaning houses to support the children. It was while feeding the pigs on his grandfather’s farm in north Taranaki that David ruminated over being told, at New Plymouth Boys High School, of the discovery of the structure of DNA, and he decided to study science in his final school year. An undergraduate degree in chemistry and botany at Canterbury University College introduced him to the philosophy of science. Inspired by the ideas of Karl Popper (who had been a faculty member during the war), David would often quip to students, “never believe your hypotheses, use them to generate tests”.

In the early 1960s, David undertook a PhD in botany at Yale, where he became fascinated with Jacob and Monod’s descriptions of how genes worked and was influenced by G. Evelyn Hutchinson’s education philosophy that “our job is to turn you into better biologists than we are”. After a brief postdoctoral position at McMaster University, Canada, he returned to New Zealand and joined the Department of Plant Biology at Massey University in 1967. At Massey, David and his wife Pauline continued their research from Yale on plant hormones. Outside of science, David and Pauline founded a Massey (‘Fitzherbert’) branch of the Labour Party, ran local election campaigns and even rewrote the constitution of the party with future New Zealand Prime Minister, Helen Clark. Their activism decried New Zealand’s involvement in the Vietnam war, supported the Women’s National Abortion Action Campaign, and opposed both the tacit support for apartheid of All Blacks rugby tours and nuclear-armed ships in New Zealand ports.

David’s focal shift from plant physiology to evolutionary biology was inspired by Fitch and Margoliash’s 1967 Science paper1 that used protein sequences to infer evolutionary trees. In 1974, David struck up a casual conversation with one of us (M.D.H.) about connections between mathematics and biology. David noted that creationists were highlighting the assertion in Popper’s 1976 autobiography that Darwinism is not a testable scientific theory. In response to a Nature editorial2 that argued that evolution is a metaphysical theory, and so not open to falsification, David proposed a testable prediction of evolution — namely, that different proteins compared across mammal species should share the same evolutionary history3. Because a complete search of the nearly 35 million potential trees was beyond the computational capacity of available computers, David programmed a branch and bound search method to find the most parsimonious trees and (with M.D.H.) developed a theoretical distribution of trees. This work demonstrated that trees reconstructed from different proteins were more similar than could be explained by chance, and thus substantiated a unique prediction of Darwin’s theory of descent. The branch and bound algorithm4 and tree distribution metrics5 have since been incorporated in many other studies.

David’s 40-year research collaboration with M.D.H. attracted students and colleagues from mathematics, computer science and statistics to interact with those from biology, with a focus on comparative genomics. These collaborations spawned methodological insights and developments that have been critical for evolution studies, such as a Hadamard transform analysis to summarize all of the signals in the data and directly calculate branch lengths in trees6. Presenters at David’s weekly laboratory meetings were encouraged to make near-impromptu presentations that should be understood by researchers in all disciplines. In 1996, David initiated an annual week-long phylogenomics workshop in New Zealand to encourage cross-disciplinary interaction. The ongoing success of these retreats has made New Zealand a key international hub for phylogenetics research.

Advances in phylogenetic inference facilitated two recurrent, related themes in David’s work — his dictums that Darwinian microevolutionary processes underpin macroevolution and that biological processes such as competition have an active role in shaping evolution (rather than passively waiting for physical changes in the environment). This is exemplified by his molecular clock studies. It had been widely accepted that mammal and bird groups radiated following an asteroid strike and extinction of dinosaurs at the Cretaceous–Palaeogene boundary. David and collaborators analysed mitochondrial DNA, which showed that the diversification of modern mammal and bird lineages had in fact begun well before the end of the Cretaceous7. This research also revealed that some iconic Gondwanan taxa — such as moa — had not been bound to continental drift (as had been assumed), but had flown to New Zealand and later evolved into flightless giants8.

David served as president of The Society for Molecular Biology and Evolution, the Society of Systematic Biologists and the New Zealand Association of Scientists. He published impactful papers that evaluated New Zealand’s science policy and critiqued a New Zealand Treasury paper that had argued against government assistance for science research and development. As a founding co-director of the Allan Wilson Centre for Molecular Ecology and Evolution (2002–2008), he and M.D.H. led one of the most successful and productive of the New Zealand Centres of Research Excellence. In 2001, David was awarded the highest honour of the New Zealand Association of Scientists — the Marsden Medal for outstanding service to science. In 2004, he was awarded The Rutherford Medal by the Royal Society of New Zealand for outstanding contributions to New Zealand society and culture. In 2018, David was also named a foreign associate of the National Academy of Sciences.

David was unerringly generous and humble to a fault, but never missed an opportunity for an amusing quip. He once remarked to a PhD student (B. Holland) that “to prove your supervisor wrong once is a tragedy, to do it twice is carelessness”. Even as a senior professor, he was only too happy to share an office with his students, and often worked late into the night in the affectionately dubbed ‘Boffin lounge’. He would invite cash-strapped students to dinner to discuss their latest results or a manuscript, and — despite the ‘tyranny of distance’ so often felt by New Zealand-based researchers — he created opportunities for his students to work with other great scientists across the globe. He would often ask “can we be cured of science?”. So many of his former students and collaborators have long since lost all hope of a cure and continue to test evolutionary hypotheses that he helped to formulate. He is survived by his children, John and Kim, and his grandchildren Zanoor, Ari, Zoe and Freya.

Credit: Te Kunenga ki Pūrehuroa Massey University