Title
Add fish to species to let the reader know that we are talking about fishes

Abstract
Explain the abbreviations HSI, HSM in the abstract
Indicate what species abundance did you test (not an exhaustive list, just name the most important ones)

Introduction
Explain the abbreviation NMFS
State the goal of your paper in the last paragraph of introduction. As of now, the reader does not understand what is your goal, and why are you doing this research.

Methods and Results
At the beginning you should sum up the results of the entire manuscript that you have obtained in the whole study. And answer the questions and hypotheses that you have set in the introduction.
The paper is quite too long and would benefit if you point where exactly should the figures and tables be put in the text.
Page 3 Line 35 – “papers published from 1997 to present” – cite some papers so the reader knows which papers you mean
Page 3 Line 47 – remove Wikipedia and cite some actual research study if possible
Page 4 Line 10 – explain what JMP is