Dr. Ayala’s influence on research and cultural debate had many forums. In the lab, he led landmark genetic discoveries that had implications in fights against diseases such as cancer and malaria. In books and lectures, he defined himself as a philosopher-scientist who sought to reconcile religious beliefs such as creationism with the worlds of quantifiable evidence such as evolution.

In a court in Little Rock in 1981, Dr. Ayala was among the high-profile witnesses in a successful case to overturn a state law that called for “balanced treatment” in the teaching of creationism and evolution.

He was among the rare science luminaries to also gain a foothold in popular culture with television appearances and books such as “Am I a Monkey? Six Big Questions about Evolution” (2010).

“My own concerns and activities are primarily centered on a scientific view of the world,” he said in 2002. “I find science rewarding and enlightening and fulfilling, but I don’t believe for a moment that science tells us all that is worth saying about the world.”

His awards included the National Medal of Science and the Templeton Prize, given for work bridging science and wider questions facing humanity and which comes with a purse of $1.5 million.

His reputation unraveled in 2018 after sexual-harassment allegations by four women — three faculty members and one graduate student — led to a probe by the University of California at Irvine, where he worked since 1987 and was a multimillion-dollar donor. Dr. Ayala resigned, and the university removed his name from its School of Biological Sciences, a science library and other programs.

Dr. Ayala denied the claims by the women but expressed regret that his conduct was interpreted as offensive. He described himself as reflecting “the good manners of a European gentleman,” such as greeting people with a customary kiss on both cheeks or to “compliment them on their beauty.”

A university investigation detailed incidents such as Dr. Ayala commenting on the size of a pregnant woman’s belly and inviting a female subordinate to sit his lap during a crowded meeting.

The National Academy of Sciences rescinded Dr. Ayala’s membership in 2021 for violation of its code of conduct.

Respecting science and religion

Dr. Ayala said he was thrust into the intellectual mine field between science and religion after leaving the Dominican order and emigrating in 1961 to the United States. He was startled at the power that creationism and other religious beliefs had on public and political discourse.

Dr. Ayala always emphasized his respect for religion and its role as a moral and cultural compass — while also remaining vague about how much of his former Catholic life he retained. Yet he passionately argued against biblical literalism and other views such as intelligent design, which professes that the natural world is too complex to have developed without the guiding hand of a supreme being.

His views of faith and scientific were closely aligned with Pope John Paul II’s message in 1996 to the Pontifical Academy of Sciences, describing evolution as “more than just a theory” but calling the human soul divinely created and unique in each person.

Religion, Dr. Ayala said, seeks to explain the meaning and purpose of life, including a relationship with a perceived higher power. Science puts theories to the test to create a how-to manual on the cosmos as knowledge and expertise grows.

“They deal with different ways of knowing,” he told the New Scientist. “I feel that science is compatible with religious faith in a personal, omnipotent and benevolent God.”

For more than five decades, Dr. Ayala spearheaded a body of work and research that explored different expressions of evolution — some accelerated and some static — and helped teams that searched back in time like molecular detectives to postulate on the first case of malaria in humans.

In the lab, Dr. Ayala developed a new genetic species of the common fruit fly, whose super-fast reproduction is used in testing and developing potential cancer drugs and gene therapies in humans. He also led a scientific forensics team that determined malaria was passed from chimpanzees to humans, perhaps through a single mosquito, between 5,000 and 6,000 years ago.

A 2010 paper he co-authored said that gorillas and chimps may now serve as “reservoirs” for the parasites that cause human malaria. That means even if a vaccine is developed, humans will always be vulnerable to reinfection as the parasites evolve in primates.

Other critical research uncovered the mirror-image DNA among the parasite that causes Chagas’ disease, which can cause irreversible damage to the heart and digestive organs if left untreated. Dr. Ayala found that parasite uses a process of DNA cloning rather than normal reproduction. The discovery opened new insights into atypical evolution and how to develop strategies to potentially control the parasite, which is prevalent in Latin America.

In 2010, Dr. Ayala referenced Pablo Picasso’s 1937 painting “Guernica” while accepting the Templeton Prize.

Dr. Ayala said “Guernica,” which depicts the 1937 bombing of the city of Guernica during the Spanish civil war, helps explain his views of faith and science as parts of the same whole. Science, he said, can explain the painting’s constituent parts of pigments and canvas and other elements. Only a spiritual lens, he said, can grasp the horrors and misery Picasso conveyed.

“Together,” he explained, “these two separate analyses reveal the totality of the masterpiece.”

Brief priesthood

Francisco José Ayala Pereda was born in Madrid on March 12, 1934, in a family he described as “reasonably well-to-do” through his father’s job as a successful businessman. Dr. Ayala took an early interest in science from a grade-school teacher whose emotions, he said, would “catch fire” when explaining the natural world.

He graduated from the University of Madrid in 1955 and studied philosophy and theology at the University of Salamanca until 1960, when he was ordained a priest but was already “disillusioned” with a life within the church. He left the priesthood the same year.

Dr. Ayala said he was highly influenced while studying in Salamanca by the 1955 book “The Phenomenon of Man,” a seminal work by geologist and Jesuit priest Pierre Teilhard de Chardin, overlaying religion and Charles Darwin’s studies of evolution.

“Evolution was the subject to which I wanted to dedicate my life,” he said.

Dr. Ayala moved to New York for studies at Columbia University, receiving his master’s degree in 1963 and doctorate in 1964 under the mentorship of Theodosius Dobzhansky, a pioneering geneticist. Dr. Ayala became a U.S. citizen in 1971.

He accepted a position in 1971 at the University of California at Davis, then shifted to the system’s Irvine campus in 1987. He received the National Medal of Science in 2001. In 2011, he bestowed $10 million to the university’s School of Biological Sciences. Some of his income came from a vineyard in Northern California. He also served as a chairman of the board at the American Association for the Advancement of Science.

He wrote or co-authored more than 25 books including “Darwin’s Gift to Science and Religion” (2007), in which Dr. Ayala expounded on his idea that only evolution can explain “the problem of evil.”

“As floods and drought were a necessary consequence of the fabric of the physical world, predators and parasites, dysfunctions and diseases were a consequence of the evolution of life,” he wrote. “They were not a result of deficient or malevolent design; the features of organisms were not designed by the creator.”

His marriage to Mary Henderson ended in divorce. In addition to his wife of 38 years, the former Hana Lostakova, survivors include two sons from his first marriage and four grandchildren.

Dr. Ayala was mostly earnest and respectful in his sparring with proponents of religious text on creation. He could at times work in a flippant jab or two. In a 1999 interview, he went off on creation traditions, going back to Greek mythology, of humans formed from clay.

“Why is it better to come from clay?” he told the Los Angeles Times. “Monkeys and apes are lovely animals, in my book. They’re much better than clay.”