Hello Zhao; Like you, I sample ants using pitfall traps. I try to estimate diversity in various habitats. Here are some of the issues I pay attention to.

1. To make valid comparisons, sampling effort (number of trap nights) in each sampled area must be comparable. Otherwise the more intensely sampled area will show higher diversity.

2. As you have done, Incidence data should be used in your analysis. Otherwise the most common species overwhelm the numbers of the rarer species.

3. I use a saturation curve for two reasons. The first is to get some indication of when my sampling has reached an asymptote. The second reason is that it, like the Chao Estimates, estimates the number of undetected, rare species. You can see how I did that by looking up this paper (available at ResearchGate).

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Des Lauriers, James & Dana lkeda, 2017. The Ants {Hymenoptera: Formicidae) of the San Gabriel Mountains of Southern california, usA with an Annotated List. p 264-217. lN: Reynolds, RE {ed}, 20L7. Desert Studies Symposium. california state University Desert Studies Consortium .342 pp.

Good luck with your project, Jim Des Lauriers

I think you can use the Vegan package in R to include phylogenetic diversity in your analyses: https://cran.r-project.org/web/packages/vegan/vegan.pdf