It is probably a bad idea to split such closely related data into separate arrays. Use a hash of arrays.

my %location_data;
foreach  (@values) {
    my @vals = split /,/, $_;
    push @{$location_data{lat}}, $val[0];
    push @{$location_data{lon}}, $val[1];
}
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Depending on how you use the data, it may be more convenient to have an array of coordinate pairs. (Like you already have except each pair would be stored as a two element numeric array rather than as a string.

my @locations = [map {split /,/, $_]} @values;
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