Does anyone know why Arduino calls a USB connection a serial? When I hear a serial connection I automatically think of a male pin connection and not a USB connection. Also not sure if this a Linux term or just an Arduino thing.
As @ratchetfreak answered, USB is a Serial bus. But there is more.
The microcontroller on Arduino boards has one or more built-in peripherals called
UARTs, which stands for Universal Asynchronous Receiver-Transmitter.
This is what the Arduino core calls a Serial port. It uses the same kind of protocol as the old DB-9 serial ports on PCs and such, but at 5V or 3.3V logic levels. Contrast this 0V to 5V voltage swing to indicate Logic LOW and Logic HIGH with the RS-232 standard for the old PC serial ports, which use a +12V to -12V swing to indicate such.
But PCs today don't often have the old RS-232 serial port. They instead have the new USB - Universal Serial Bus - port. On the Arduino board is chip that communicates on one side via USB with the PC and tells the PC that it provides the equivalent of the old COMPORT or /dev/ttyS* serial device; and on the other side via UART with the microcontroller on the Arduino board.
It's like we are "emulating" the old PC serial ports in software over the new USB bus, which itself is a serial communication system, though much more complex than a plain UART.
On most Arduinos
Serial is not a USB connection. It is a UART (real serial) connection which is used to communicate with a USB to UART adaptor (often made out of another small MCU, the ATMega16U2). It's only from that chip onwards that it is USB. Between the main MCU and that USB interface chip it is serial. The same serial you get from pins 0/1 (literally: it's hardwired together).
Indeed, the first Arduino prototype (that grew out of the Wiring project) had no USB at all - only Serial. The USB to UART adaptor was added later. But it still remains a Serial interface.
Almost all the ways protocols used to communicate on arduino are Serial. USB,UART, I2C, SPI. Serial means one bit at a time, then the other way is Parallel communication which is what printers used to use. This allowed a whole byte to sent at one time(there were 8 data lines). As clock speeds increased there was no longer a need to have these big bulky,expensive cables and connectors. So away went parallel connections from common computer/electronics applications.