Understanding factors driving diversity across biodiversity hotspots is critical for formulating conservation priorities in the face of ongoing and escalating environmental deterioration. While biodiversity hotspots encompass a small fraction of Earth’s land surface, more than half the world’s plants and two-thirds of terrestrial vertebrate species are endemic to these hotspots. Tropical Southeast Asia displays extraordinary species richness, encompassing four biodiversity hotspots, though disentangling multiple potential drivers of species richness is confounded by the region’s dynamic geological and climatic history. Here, we use multi-locus molecular genetic data from dense multi-species sampling of freshwater fishes across three biodiversity hotspots, to test the effect of Quaternary climate change and resulting drainage rearrangements on aquatic faunal diversification. While Cenozoic geological processes have clearly shaped evolutionary history in Southeast Asian halfbeak fishes, we show that paleo-drainage re-arrangements resulting from Quaternary climate change played a significant role in the spatiotemporal evolution of lowland aquatic taxa, and provides priorities for conservation efforts.
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FIGURE S1. Temporal Dermogenys+Nomorhamphus dynamics among paleo-drainages.
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FIGURE S2. Individual mitochondrial and nuclear gene trees for Dermogenys+Nomorhamphus and Hemirhamphodon.
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FIGURE S3. Dermogenys+Nomorhamphus geographic range evolution.
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FIGURE S4. Hemirhamphodon geographic range evolution.
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FIGURE S5. Dermogenys+Nomorhamphus species tree based on taxonomy (A) (Collette 2004; Meisner 2001) and a priori paleo-drainage designation (B) (Voris 2000).
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FIGURE S6. Hemirhamphodon species tree based on taxonomy (A) (Anderson and Collette 1991) and a priori paleo-drainage designation (B) (Voris 2000).
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FIGURE S7. BEAST Analyses run with and without data to examine the influence of the priors. Solid lines are prior distributions, shadow densities are posteriors on 'empty' data.
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TABLE S1. Sampling locations and sample information for this study.
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TABLE S2. Genbank accession numbers for this study.
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Table S3. mtDNA Control region: Maximum Likelihood fits of 24 different nucleotide substitution models
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Table S4. mtDNA COI: Maximum Likelihood fits of 24 different nucleotide substitution models
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Table S5. DP5: Maximum Likelihood fits of 24 different nucleotide substitution models
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Table S6 DP14: Maximum Likelihood fits of 24 different nucleotide substitution models
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Table S7. DP21: Maximum Likelihood fits of 24 different nucleotide substitution models
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Table S8. DP35: Maximum Likelihood fits of 24 different nucleotide substitution models
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Table S9. DP37: Maximum Likelihood fits of 24 different nucleotide substitution models
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Table S10. HP5: Maximum Likelihood fits of 24 different nucleotide substitution models
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Table S11. HP54: Maximum Likelihood fits of 24 different nucleotide substitution models
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Table S12. HP56: Maximum Likelihood fits of 24 different nucleotide substitution models
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TABLE S13. Dermogenys+Nomorhamphus geographic range evolution.
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TABLE S14. Hemirhamphodon geographic range evolution.
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TABLE S15. Bayes Factors (BF) of mtDNA Bayesian phylogeographic analyses of diffusion rates in Southeast Asian halfbeaks (Dermogenys+Nomorhamphus).
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TABLE S16. Bayes Factors (BF) of mtDNA Bayesian phylogeographic analyses of diffusion rates in Southeast Asian halfbeaks (Hemirhamphodon).