The signal is similar to one seen by the NASA's Fermi Gamma-ray Space Telescope at the centre of our own Milky Way galaxy in 2014.
Gamma rays are the highest-energy form of light, produced by the universe's most energetic phenomena.
They are common in galaxies like the Milky Way because cosmic rays, particles moving near the speed of light, produce gamma rays when they interact with interstellar gas clouds and starlight.
To explain this unusual distribution, scientists are proposing that the emission may come from several undetermined sources. One of them could be dark matter, an unknown substance that makes up most of the universe.
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"We expect dark matter to accumulate in the innermost regions of the Milky Way and other galaxies, which is why finding such a compact signal is very exciting," said Pierrick Martin, an astrophysicist at the National Centre for Scientific Research and the Research Institute in Astrophysics and Planetology in France.
Another possible source for this emission could be a rich concentration of pulsars in M31's centre. These spinning neutron stars weigh as much as twice the mass of the sun and are among the densest objects in the universe.
One teaspoon of neutron star matter would weigh a billion tons on Earth. Some pulsars emit most of their energy in gamma rays. Since M31 is 2.5 million light-years away, it is difficult to find individual pulsars.
To test whether the gamma rays are coming from these objects, scientists can apply what they know about pulsars from observations in the Milky Way to new X-ray and radio observations of Andromeda.
"We don't fully understand the roles cosmic rays play in galaxies, or how they travel through them," said Xian Hou, an astrophysicist at Chinese Academy of Sciences.
"M31 lets us see how cosmic rays behave under conditions different from those in our own galaxy," said Hou.
The similar discovery in both the Milky Way and M31 means scientists can use the galaxies as models for each other when making difficult observations.
While more observations are necessary to determine the source of the gamma-ray excess, the discovery provides an exciting starting point to learn more about both galaxies, and perhaps about the still elusive nature of dark matter.
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