What helped ID Joseph Augustus Zarelli? His mother’s family dabbles in genetic genealogy.

It’s the ultimate rabbit hole of hobbies: genetic genealogy.

There are legions of self-taught ancestry bloodhounds who upload their DNA to multiple databases in search of kin who did likewise, plugging gaps in their family tree.

Joseph Augustus Zarelli’s biological mother had third and fourth cousins who did just that. They had uploaded their DNA to GEDmatch — a database that law enforcement and forensic scientists can access to help solve cold cases.

It was those cousins who planted the first seeds that led Misty Gillis, a forensic genetic genealogist and cold-case liaison with Identifinders International, to grow branches that reached all the way to Zarelli’s birth mother, Gillis said, thus putting a name to the “Boy in the Box.”

“On the maternal side, I used a whole bunch of third and fourth cousins that I was able to build out their genetic trees and see where they married into,” Gillis said by phone this week. “And so I built those trees down and down, painstakingly. It took me about two months until I was able to identify who the birth mother was.”

» READ MORE: Waves of speculation followed the release of Joseph A. Zarelli’s name

Gillis’ identification in early 2021 of Joseph’s mother — whose identity the police continue to guard closely —was a big break in the nearly 65-year-old case, one of the Philadelphia Police Department’s oldest active homicide investigations. Armed with the mother’s name, detectives got a court order to obtain the boy’s birth certificate.

Joseph Augustus Zarelli was born Jan. 13, 1953, to a woman who was not married to Joseph’s father during an era when out-of-wedlock births carried a tinge of shame. Although the name of the father appeared on the birth certificate, the name alone wasn’t proof that he was Joseph’s biological father, Gillis said. That would take more DNA digging.

“We had the mom already, so it was the dad’s side we had to work on,” Gillis said. “So I had to call relatives on the dad’s side and see if they would upload their DNA.”

Gillis said her first call was to Justin Thomas, who she believed was a relative of Joseph’s on the Zarelli side.

“You might be a match to a cold case in Philadelphia,” Gillis said she told Thomas during a phone call that took place more than a year ago. In an interview last week, Thomas said he had taken a DNA test with Ancestry.com for fun in 2017 and Gillis had called him “out of the blue” and said he was a match in a Philadelphia cold case.

In an interview this week, Gillis said Thomas had “misremembered” a little of what happened. She said she was not able to access his DNA through Ancestry.com, which restricts law enforcement use.

“I thought he was a match and that’s why I reached out to him to ask if his family would consider taking a test,” Gillis said. “I want it to be clear that I didn’t use Ancestry. It’s been over a year, so he probably doesn’t remember how things happened and he’s probably dealing with some shock himself as well.”

Gillis said she never revealed Joseph’s name, and outside of a tiny circle of investigators working directly on the case, Thomas — along with the world — learned the boy’s identity during last week’s news conference at Police Headquarters on North Broad Street. Police had found Joseph’s battered and malnourished body inside a cardboard box in a weedy lot in the city’s Fox Chase section in February 1957. He had just turned 4.

Both Gillis and Thomas agree, however, that Thomas put Gillis in touch with his mother — believed to be a first cousin of the boy. She agreed to upload her DNA to GEDmatch, the same database used by law enforcement in 2018 to determine the identity of the Golden State Killer.

Thomas’ mother was a DNA match to the boy. But first cousins share 12.5% on average of the so-called “autosomal DNA, which forms the bulk of the genome — 22 out of the 23 pairs of chromosomes. While the average is 12.5%, the range is quite large: about 4% to 23%, according to 23andMe, a popular ancestry site.

» READ MORE: The boy's body was exhumed on two occasions to extract DNA, in 1998 and 2019.

Gillis said investigators are “100% certain” that the people listed on Joseph’s birth certificate were his biological parents, both now deceased. She declined to provide additional details, saying only, “We had other DNA sources [besides Thomas’ mother] that were able to verify it.”

Police authorities have said that Joseph has living half-siblings on both his maternal and paternal side. Investigators declined to name the boy’s parents or his half-siblings during the news conference.

Gillis, who is 34 and works out of her Chicago home, became enchanted with genealogy when she was a teenager. In her late 20s, as genetic testing evolved, she had her father take a DNA test and used it to identify her grandfather’s father. “Once I did that, I was absolutely hooked,” she said.

Gillis said she thought of the then-unidentified Joseph as her own son. When she nailed down his identity in fall 2021, she erupted in tears.

“I cried for about three days straight because I felt like I could finally grieve him,” said Gillis, who has three children of her own, ages 10, 7, and 5. “When I work these cases, it’s like you’re walking alongside the person silently. … It was really emotional for me, but it was closure in a sense. I take these kids on as if they are my surrogate children. I feel like I’m [Joseph’s] mom in a sense and I have to bring him home.”

During her nearly four years working as an independent contractor with Identifinders International, founded by forensic scientist Colleen Fitzpatrick, Gillis said she’s helped solve 17 cases. Law enforcement agencies nationwide contract with Fitzpatrick’s company to work old murder cases. Perhaps one of Gillis’ most widely known solves was the “Baby Holly” case out of Texas. The baby and her parents went missing in 1980. The bodies of two adults were found in a wooded area in Houston in 1981, but their names were not known. Last year, Gillis identified the murdered couple as Tina Gail Linn Clouse and Harold Dean Clouse Jr.

“We called the family and they said, `What about their daughter, Holly?’” Gillis recalled. “It turns out she was adopted out and she’s been located and reunited with her family.”

It took years for Fitzpatrick and other forensic scientists to “knit” the DNA of Joseph back together.

“DNA is a big molecule,” Fitzpatrick said last week after the news conference. “It just completely shatters. It breaks apart. It’s exposed to humidity, the acid in the soil, rain, temperature, heat. When we got the DNA, it was basically just confetti.”

In spring 2021, Fitzpatrick and her peers finally stitched the degraded DNA into a usable form. They uploaded the boy’s genetic profile to GEDmatch, Fitzpatrick said. That’s how Gillis found matches to third and fourth cousins on Joseph’s mother’s side.

So why would those cousins — or anyone — upload their DNA to GEDmatch? Gillis explained that people who are curious about their genealogy often send their DNA to databases, like Ancestry or 23andMe. The really passionate will take the extra step of uploading their DNA to GEDmatch.

“A lot of genealogists who have taken DNA tests are aware of GEDmatch because GEDmatch can be used to get better results for their own DNA tests,” Gillis said. “It’s not just for law enforcement. It’s for hobbyists.”

Staff writers William Bender and Tom Avril contributed to this article.