I like to scale them in towards each other just to make selecting the vertices easier.

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Select the Vertices of the edge you just extruded

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Merge them together.

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Now move the final vertex down in the Y direction to make a flat cap for the tree trunk.

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Now we are going to Unwrap the UVs so later on we can apply a texture to the tree. Select the trunk in Object Mode and apply Cylindrical Mapping.

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Now Select the top faces of your trunk and from the Top Viewport apply Planar Mapping.

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