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What evidence suggests that Proto-Niger-Congo had a noun class system?

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Thematic map of Africa showing the distribution of Niger-Congo language branches. Distinct colors represent language groups such as Atlantic, Mande, Gur, Kwa, Benue-Congo, and Bantu, with Bantu languages covering most of central, eastern, and southern Africa. A numbered key lists prominent languages in each area, and country borders are marked for reference. — Niger-Congo languages Map showing the branches and distribution of the Niger-Congo languages.

Most linguists accept the probability that Proto-Niger-Congo possessed a noun class system, even though not all modern languages in the family have retained it. The evidence for this reconstruction is based on the widespread presence of noun class systems across the various branches of the Niger-Congo family.1

Key indicators supporting this include:

Widespread Distribution: Noun class systems, characterized by nouns marked with specific affixes (prefixes, suffixes, or both) to signal singular and plural forms, are found in some form in every branch of the Niger-Congo family.1
Concordial Systems: Many languages exhibit an accompanying system of agreement (concord), where other elements in a clause—such as adjectives, determiners, numerals, and verbs—are marked with affixes that correspond to the class of the noun.1
Partial Retention: Many languages that do not possess a full system still show traces of it, such as a reduced number of classes or remnants of concordial features.1

While semantic categories likely originally determined these classes, these meanings have largely broken down over time, making the systems formal rather than semantic in most contemporary languages.1