Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses

Area of Science:

• Evolutionary Biology
• Ecology
• Genomics

Background:

• Species persistence relies on ecological dynamics, while proliferation occurs via evolutionary mechanisms.
• Dated molecular phylogenies and DNA sequencing reveal significant cryptic diversity, especially in species-rich areas.
• Explicit eco-evolutionary diversification models are now available.

Purpose of the Study:

• To investigate diversification trajectories in 10 Sundaland freshwater fish lineages.
• To assess the impact of cryptic diversity on diversification model selection and inferences.
• To explore the drivers and patterns of cryptic diversification.

Main Methods:

• Utilized time-calibrated, taxonomically rich phylogenies for 10 freshwater fish lineages.
• Applied DNA-based species delimitation methods to identify cryptic diversity.
• Fitted various diversification models to the phylogenies, comparing results with and without cryptic diversity.

Main Results:

• Eight clades showed a constant speciation rate model as most likely when cryptic diversity was included.
• Nine clades exhibited signatures of diversification slowdowns when cryptic diversity was ignored.
• Most cryptic diversification occurred within the last 5 million years, driven by geographical isolation.

Conclusions:

• Cryptic diversity significantly influences diversification model selection, often masking constant speciation rates.
• Geographical isolation in homogeneous landscapes appears to be a primary driver of cryptic lineage diversification.
• The findings raise questions about the persistence and role of cryptic diversity in overall species proliferation.