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Species delimitation is challenging in sibling species/cryptic lineages because of the absence of clear diagnostic traits. However, integration of different approaches such as phylogeography and ecological niche comparison offers one potential approach to tease apart recently diverged lineages. In this study, we estimate the ecological niche divergence among lineages in  Chromis viridis  in a broad-scale phylogeographic framework to test whether the combination of these two approaches can effectively distinguish recently diverged lineages. Results from Cytb and Rag2 analyses identified two cryptic lineages ( C. viridis A  and  C. viridis B ) that diverged ∼3 Myr ago. Estimates of ecological niche divergence with 11 environmental parameters across the broad geographic range of these lineages showed overlapping ecological niches and niche conservatism. However, regardless of the incongruence between genetic and ecological niche divergence, the substantial genetic divergence between the two clades of  C. viridis  in both mtDNA and nuclear loci strong suggest that they are cryptic taxa.

Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (Chromis viridis)