Did Captain Ezekiel “Zeke” Harper have an illegitimate child?

Captain Ezekiel “Zeke” Harper was a Confederate guerrilla scout during the American Civil War. Zeke spent his youth exploring the high Alleghenies (part of the Appalachian Mountain Range) near his home in West Virginia. In his mid-twenties, Zeke traveled across the country to the California gold fields and became known as a lead war scout and mountain guide. In California and Oregon, he prospered as a cattle baron, miner, property owner and merchant.

Just prior to the American Civil War, Zeke returned to West Virginia and immediately began helping the Confederates as a guide and scout in the Alleghenies – a region he knew well from his youth. During the American Civil War, Zeke and his older brother, Bill, became two of the most famed scouts in the region, until 1863 when Zeke was captured and Bill was killed.

Did Zeke have an illegitimate child?
Shortly after his imprisonment, Zeke was traded back to the Confederates and he returned to Tucker Country after the Civil War. He became a well-known country doctor and a landowner of approximately 4500 acres. During the late 1870s or 1880s, it was rumored that Zeke fathered a child with his Native American maid. In 1892, Zeke kindly opened his door to some cold, wet strangers. These men turned out to be robbers who clubbed him senseless and threw him in the outhouse. He was discovered a few hours later but died from his injuries.

Zeke’s alleged son, Earl J Maxwell, was sent to a local orphanage, but Zeke’s girlfriend prior to the Civil War managed to track him down and raised him as one of her own. Earl had seven children who grew up hearing stories about their grandfather Zeke Harper. After Earl’s death, an investigation began to determine if Zeke was the true biological father of Earl.

Exhumation of Zeke’s Remains
The investigators were granted permission to exhume the body of Zeke Harper from the family cemetery. During the exhumation process, the investigators discovered that Zeke had been buried in a wooden casket with an inner glass casing. Although by the time of the exhumation (120 years post-burial) both casings had deteriorated and collapsed, it is likely that for a long period, the extra layer provided some protection to the remains and DNA. Several different bone samples were collected for genetic analysis.

Genetic analysis of Zeke’s skeleton
The best way to confirm father-son relationships is by the comparison of Y-DNA markers. Y-DNA is passed down from father to son along the direct paternal lineage; so all males who have descended from the same paternal lineage are expected to have exactly the same or a very similar Y-DNA profile. Hence, the Y-DNA profile of Zeke (determined from DNA extraction from his remains) should match to the Y-DNA profile of two living paternal descendants of his alleged son, Earl J Maxwell. Seventeen Y-STR markers were examined using extracts from the bone samples of Zeke. This Y-DNA profile was an exact match (at all 17 loci) to the Y-DNA profile determined from buccal samples collected from two paternal grandsons of Earl.

Conclusions
The Y-DNA profile obtained from Zeke’s skeleton is identical to the Y-DNA profile of two paternal grandsons of Zeke’s alleged son, Earl. This particular Y-DNA profile was also not found in either of two Y-STR databases, indicating that it is a relatively rare genetic profile. This genetic match between Zeke and his putative paternal descendants is strong evidence that Earl J Maxwell was an illegitimate child of Zeke Harper.