What do the paranthesis and $ sign mean in echo $(ls)

This is command substitution for bash.

Command substitution allows the output of a command to replace the command itself. Command substitution occurs when a command is enclosed as follows:
 $(command) or

 `command`

http://www.gnu.org/software/bash/manual/bashref.html#Command-Substitution

http://tldp.org/LDP/abs/html/commandsub.html

http://wiki.bash-hackers.org/syntax/expansion/cmdsubst

And a good example similar to your question:

http://bashshell.net/shell-scripts/using-command-substitution-in-a-bash-shell-script/

When the shell encounters text enclosed in $( ), it:

Takes it to be a command and (as Panther says) runs the command in a subshell.
Substitutes the output of the command, in place of the entire $(...) expression. Any trailing newlines are removed from this output.
Performs further expansions if $(...) was not quoted (see below).

As heartsmagic's answer explains, this is one of two available syntaxes for command substitution.

"What ... causes the output of these two commands to be the same?"

It's actually somewhat uncommon for the output of ls to be exactly the same as the output of echo $(ls):

ek@Io:~/tmp$ ls
bar  foo
ek@Io:~/tmp$ echo $(ls)
bar foo

ls typically separates filenames by two or more spaces, or a newline. This helps us tell them apart more easily, especially since spaces in filenames are somewhat common (but multiple consecutive spaces, less common).

Word Splitting

When I ran echo $(ls), the following happened.

Command substitution replaced $(ls) with:
```
bar
foo
```
You might be surprised to hear that, since that's probably not what you see when you run ls by itself! This disparity in what ls outputs is explained below, but is actually not the reason you end up with a single space between those two words. The same thing would happen if $(ls) were substituted with bar foo (with two spaces).
Afterwards, the shell performed word splitting, treating bar and foo as separate arguments to the echo command instead of as a single argument containing spaces.

Globbing (a.k.a. filename/pathname expansion) would also be performed, if the command's output had contained *, ?, or [.

As detailed below, quoting with double quotes permits command substitution but suppresses word splitting and globbing.

When echo receives multiple arguments (except for options like -n, which are treated specially and not printed at all), it prints them all out, with a single space between subsequent arguments. echo then prints a newline, unless the -n option was passed.

Thus echo $(ls) shows output like bar foo instead of bar foo.

If you run ls and it lists no files, or just one file, the output of ls will often be the same as the output of echo $(ls). Even then, it will not always be the same, such as when a filename contains whitespace other than isolated (single) spaces:

ek@Io:~/tmp2$ touch 'my   file'
ek@Io:~/tmp2$ ls
my   file
ek@Io:~/tmp2$ echo $(ls)
my file

When ls prints multiple files, its output is not likely to be exactly that same as the output of $(ls). Similarly:

echo a b and echo $(echo a b) produce the same output, but
echo 'a b' and echo $(echo 'a b') do not.

This is an important thing to know about command substitution--unquoted command substitutions are subject to word splitting (and globbing).

Quoting

If you want to prevent word splitting and globbing--and you usually will want to prevent them--you can enclose your expression for command substitution in double quotes (" "). The reason to use double quotes rather than single quotes is that single quotes are even stronger; they would suppress command substitution.

This also applies to parameter expansion, which is a more commonly used shell expansion than command substitution, and to arithmetic expansion. The reasons it is important to quote command substitutions (except in the fairly uncommon) case that you know you want further expansions to occur) are the same as the reasons to quote parameter expansion.

Terminal Detection

Double-quoting often sufficient to avoid unexpected results from command substitution. In particular, it will work with the echo-based examples above as well as the example of ls on a directory with a single entry containing spaces:

ek@Io:~/tmp2$ echo "$(ls)"
my   file

However, as noted above, you might be surprised to find that what you see when you run ls is often not what gets passed to echo in place of "$(ls)":

ek@Io:~/tmp$ ls
bar  foo
ek@Io:~/tmp$ echo "$(ls)"
bar
foo

This is because ls checks if standard output is a terminal to decide how to format its output, when output formatting is not explicitly specified.

When stdout is a terminal, ls outputs in vertically sorted columns, like ls -C.
When stdout is not a terminal, ls lists each entry on its own line, like ls -1.

In command substitution, standard output isn't a terminal because the command's output is not being sent directly to a terminal for you to see--instead, it is being captured by the shell and used as part of another command.

To get multi-column formatting when running ls via command substitution, pass it the -C flag:

ek@Io:~/tmp$ echo "$(ls -C)"
bar  foo

(dir is sometimes suggested as an alternative to ls -C and will also work for this, though dir behaves like ls -C -b rather than merely ls -C.)

Shell Aliasing

Another reason ls may sometimes behave differently from echo "$(ls)" is that ls may be a shell alias. Run alias ls to check; on Ubuntu you usually get alias ls='ls --color=auto'. This makes it so that, when ls appears as the first word of a command you run interactively (and also in the far less common situation that alias expansion has been enabled in a non-interactive shell), it is replaced with ls --color=auto.

For example, when I run ls, it lists directories colored blue and executables colored green (and observes many other coloring rules, too). --color=auto causes ls to print colored output when standard output is a terminal, and not otherwise.

To get colored output when running ls via command substitution, pass it the --color or --color=always option. If you like, you can combine this with -C:

echo $(ls -C --color)

Note that while you can make ls an alias to ls --color or ls --color=always instead of ls --color=auto, and ls --color=always doesn't care if standard output is a terminal... that alias will still not cause ls to produce colored output when invoked by command substitution. This is because shell aliases (in Bourne-style shells like bash) are only expanded when the shell sees them as the first word of a command, and they are not inherited by subshells.

() and $() are used to run commands in a subshell.

See http://tldp.org/LDP/abs/html/subshells.html for details.