For most marine organisms, species richness peaks in the Central Indo-Pacific region and declines longitudinally, a striking pattern that remains poorly understood. Here, we used phylogenetic approaches to address the causes of richness patterns among global marine regions, comparing the relative importance of colonization time, number of colonization events, and diversification rates (speciation minus extinction). We estimated regional richness using distributional data for almost all percomorph fishes (17 435 species total, including approximately 72% of all marine fishes and approximately 33% of all freshwater fishes). The high diversity of the Central Indo-Pacific was explained by its colonization by many lineages 5.3 -34 million years ago. These relatively old colonizations allowed more time for richness to build up through in situ diversification compared to other warm-marine regions. Surprisingly, diversification rates were decoupled from marine richness patterns, with clades in low-richness cold-marine habitats having the highest rates. Unlike marine richness, freshwater diversity was largely derived from a few ancient colonizations, coupled with high diversification rates. Our results are congruent with the geological history of the marine tropics, and thus may apply to many other organisms. Beyond marine biogeography, we add to the growing number of cases where colonization and time-for-speciation explain large-scale richness patterns instead of diversification rates.
Substantial genetic variation is found in weedy rice (Oryza sativa f. spontanea Roshev.) populations from different rice‐planting regions with the change of farming styles. To determine the association of such genetic variation with rice farming changes is critical for understanding the adaptive evolution of weedy rice. We studied weedy‐rice specific novel single nucleotide polymorphisms (SNPs) by genome‐wide comparison between DNA sequences of weedy and cultivated rice, in addition to polymerase chain reaction fingerprinting at 22 selected novel SNP loci in weedy rice populations. A great number of novel SNPs were identified across the weedy rice genome. High frequencies of the novel SNPs were determined at the 22 selected loci, although with considerable variation among weedy rice populations in different rice‐planting regions. The highest frequency (∼57%) of novel SNPs was identified in weedy rice populations from Jiangsu that experienced the most dramatic changes in rice farming styles, including the shift from transplanting to direct seeding, and from indica to japonica varieties. The lowest frequency (∼29%) was detected in weedy rice populations from Northeast China, where rice farming has undergone relatively less change. The association between frequencies of novel SNPs in weedy rice populations and the extent of changes in rice farming styles suggests the critical role of adaptive mutation and accumulation of the mutation influenced by human activities in the rapid evolution of weedy rice.
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