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a first wave from the Malay archipelago perhaps 50,000 years ago when New Guinea and Australia were a single landmass called Sahul,
and, much later, a wave of Austronesian people from the north who introduced Austronesian languages and pigs about 3,500 years ago, and who left a small but significant genetic trace in many coastal Papuan peoples (only a minority of Austronesian-speaking Papuans have detectable Austronesian ancestry).
The term "Papuan" is used in a wider sense in linguistics and anthropology. In linguistics, "Papuan languages" is a cover term for the diverse, mutually unrelated, non-Austronesian language families spoken in Melanesia, the Torres Strait Islands, and parts of Wallacea. In anthropology, "Papuan" is often used to denote the highly diverse aboriginal populations of Melanesia and Wallacea prior to the arrival of Austronesian-speakers, and the dominant genetic traces of these populations in the current ethnic groups of these areas.
The language families in Ross' conception of the Trans-New Guinea language family.
Ethnologue's 14th edition lists 826 languages of Papua New Guinea and 257 languages of Western New Guinea, a total of 1073 languages, with 12 languages overlapping. They can be divided into two groups, the Austronesian languages, and all the others, called Papuan languages for convenience. The term Papuan languages refers to an areal grouping, rather than a linguistic one. So-called Papuan languages comprise hundreds of different languages, most of which are not related.
In a 2005 study of ASPM gene variants, Mekel-Bobrov et al. found that the Papuan people have among the highest rate of the newly evolved ASPM Haplogroup D, at 59.4% occurrence of the approximately 6,000-year-old allele. While it is not yet known exactly what selective advantage is provided by this gene variant, the haplogroup D allele is thought to be positively selected in populations and to confer some substantial advantage that has caused its frequency to rapidly increase.