Tyson Fresh Meats, the world’s largest beef and pork supplier, will pay $2 million for pumping animal waste into the Missouri River, the Justice Department said Thursday. Justice said the company, a subsidiary of Tyson Foods Inc. of Springdale, Ark., violated a 2002 agreement with the government to limit its discharges into the river from a beef processing facility in Dakota City, Neb. The government said the company did not adequately treat the wastewater it discharges into the river, and as a result, fecal coliform and nitrates were discharged. Officials said the discharges caused high levels of toxicity to aquatic life in the river. Regulators said Tyson discharges an average of 5 million gallons of treated wastewater from the facility into the river each day.