Trips west
While teaching, Marsh toured the country, visiting museums to inform the planning of the Yale Museum. In 1868, he visited Cope; since their meeting, they had expressed warm wishes in letters to each other and even named species after each other. Cope took Marsh on a tour of the marl pits in New Jersey where he was finding fossils; unbeknownst to Cope, Marsh would later pay the pit operators to divert their finds to him instead. Marsh later noted that Cope's reconstruction of his newest find, the aquatic reptile Elasmosaurus, was flawed: Cope had placed the head of the animal where its tail should have been. Marsh's criticism wrankled Cope, and threatened his nascent career; he responded by critiquing errors in Marsh's work, and moving in on areas Marsh was prospecting in. Their relationship began to sour.
Marsh was looking further afield than New Jersey for fossils. While still studying in Europe, Marsh had identified the western American frontier as "the most inviting field for Paleontology in North America". In 1868, after visiting Chicago for a meeting of the American Association for the Advancement of Sciences, Marsh elected to join other members to Omaha on a "geological excursion"; it was Marsh's first trip to the far western United States, and it inspired him to return to prospect.
Plans for a prospecting trip were delayed due to conflict with Native American tribes, and Marsh's first trip started west from New Haven on June 30, 1870. The prospecting groups were formed from Yale students or recent graduates. Their path took them through Nebraska, Wyoming, Colorado, Utah, all the way to San Francisco, then back to Kansas. They were regularly escorted by companies of soldiers, including Buffalo Bill Cody and Frank North. They arrived back in New Haven on December 18. The expedition uncovered more than a hundred new species of vertebrate fossils. Marsh's papers on his finds, particularly a species of Pterosaur larger than any previously known, provided a major boost to his career. Also valuable were the personal relationships Marsh forged, the publicity the expedition had received, and the growing attention at the market for bones in the west—bones Marsh was willing to pay for.
Expeditions to areas old and new followed in 1871, 1872, and 1873. Marsh was soon joined by other scientific parties. Cope traveled to western Kansas to prospect in 1871. John Wesley Powell, Ferdinand Vandeveer Hayden and Clarence King were also traversing the American West on geological surveys. King would forward bones he found to his friend Marsh. Cope's trips into areas Marsh considered "his" territory caused their relationship to become hostile. They began attacking each other in scientific papers for perceived errors in classification or falsified publication dates, embroiling other scientists like Hayden, Joseph Leidy, and Louis Agassiz in their spats. Marsh was admitted to the membership of the National Academy of Sciences in 1872, with Cope the lone member who voted against him.
Marsh had not originally intended to do field work in 1874; by this point, he had at least twelve different groups hunting for bones on his behalf, and the Peabody Museum was under construction. Marsh was nonetheless induced to join a prospecting trip to the Black Hills of the Dakotas by personal invitation from General Edward Ord. Leaving late in the season and anticipating danger from Native Americans, Marsh relied on hired frontiersman and brought no students with him. When Marsh arrived at the Red Cloud Agency in November, the agency and tribes were locked in conflict over the matter of a Sioux census, with the lead agent refusing to disburse the tribes' annual goods without one. Marsh put his request to prospect to the council of chiefs, who considered his claim to be prospecting for fossils dubious, amid illegal gold speculation in the area sparked by George Custer's expedition into the Black Hills. While he initially got assent for the expedition, weather delays and a change in temperament led Marsh's party to withdraw to Fort Robinson, threatened by Sioux on the way. Unwilling to turn back, Marsh feted the chiefs at a banquet and again obtained permission to leave. Marsh agreed to deliver Chief Red Cloud's reports of missing supplies and corrupt government agents to Congress. Heading north to reach the edge of the Dakota badlands, Marsh's men started prospecting for fossils. The fact that they were in fact after bones and not gold led the natives employed on the expedition to call Marsh "Big Bone Chief". Warned by scouts that a hostile group of Miniconjou were planning an attack, Marsh stayed long enough to properly pack the expedition's finds before retreating south. The Miniconjou war party missed catching the expedition by less than a day.
Marsh made good on his promise in March 1875, heading to Washington and meeting with Indian Affairs commissioner Edward Parmelee Smith. Unsatisfied with Smith's explanations, Marsh arranged a meeting with President Ulysses S. Grant. Marsh was then summoned to meeting of the Board of Indian Commissioners in New York City, to which he brought a reporter, Frank Wyckoff, who wrote about the meeting in an April 30 story for the New-York Tribune. The scandal was soon overshadowed by an even greater one for the Grant Administration, the Whiskey Ring, but Marsh remained committed, publishing a 36-page pamphlet of charges and evidence in July and testifying before a special commission formed to investigate the charges. Counterattacks painted Marsh as either taken in by the natives or taking their side for his own gain—access to fossils. The special commission's report, released in October, substantiated Marsh's charges and resulted in resignations and reorganization, but did little to change government policy towards the natives. Modern scholars argue that Marsh's motives were not philanthropic, as he submitted to the generally held view of the superiority of the white race and was not fond of the native culture. Rather, his actions were likely calculated to obtain access to fossils in the Red Cloud's territory and gain publicity.
While Marsh was busy fighting the government, he continued to employ bone hunters who shipped specimens back to him, among them Benjamin Franklin Mudge and Samuel Wendell Williston. He published 19 papers on his finds between 1874 and 1876, most dealing with prehistoric mammals. He did not return west himself until 1879. In 1876, his reputation in the field was cemented during the visit by Thomas Henry Huxley, Darwin's most prominent early supporter. Huxley examined the remains of Tertiary horses amassed in the Peabody museum and realized the sequence was a prime example for gradual changing of body structure from dog-like ancestors with three hooves to modern horses. It also convinced the British naturalist that the early evolution of the horse took place in North America, not Europe as was thought previously.