Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.

Uniquely mapped reads with a mapping quality value of ≥4 were generated using SAMtools and 5.0 × 10 5 reads were used for the following analysis. The rates of false-assignment caused by pooled-PCR or sequencing steps were calculated from the numbers of ERCC-control reads in samples with and without ERCC-control (Supplementary Fig. S2). Briefly, ERCC reads detected in the late-pooled samples (without ERCC addition) were regarded as false-assignments caused by the sequencing of each sample. Therefore, the rate of total false-assignment reads in all eight samples against total ERCC reads in the lane was estimated to be the false-assignment rate caused by sequencing (Supplementary Fig. S2). The false-assignment rate caused by pooled-PCR was estimated from the ERCC-reads number detected in early-pooled samples (without ERCC addition), as explained in Supplementary Fig. S2. Estimate deviation between technical replicates in Lasy-Seq. Correlation coefficient between the early-pooled samples were calculated using rpm except for ERCC-controls to estimate deviation between technical replicates. Pearson's correlation coefficient was calculated with cor function in R version 3.5.0 52 .

The guppy (Poecilia reticulata) shows remarkable variation of photoreceptor cells in the retina, especially those sensitive to middle-to-long wavelengths of light. Microspectrophotometry (MSP) has revealed varying "green", "green-yellow" and "yellow" cone cells among guppies in Trinidad and Venezuela (Cumana). In the guppy genome, there are four "long-wave" opsin loci (LWS-1, -2, -3 and -4). Two LWS-1 alleles have potentially differing spectral sensitivity (LWS-1/180Ser and LWS-1/180Ala). In addition, two "middle-wave" loci (RH2-1 and -2), two "short-wave" loci (SWS2-A and -B), and a single "ultraviolet" locus (SWS1) as well as a single "rhodopsin" locus (RH1) are present. However, the absorption spectra of these photopigments have not been measured directly and the association of cell types with these opsins remains speculative. In the present study, we reconstituted these opsin photopigments in vitro. The wavelengths of maximal absorbance (λmax) were 571nm (LWS-1/180Ser), 562nm (LWS-1/180Ala), 519nm (LWS-3), 516nm (LWS-2), 516nm (RH2-1), 476nm (RH2-2), 438nm (SWS2-A), 408nm (SWS2-B), 353nm (SWS1) and 503nm (RH1). The λmax of LWS-3 is much shorter than the value expected (560nm) from the "five-sites" rule. The two LWS-1 alleles could explain difference of the reported MSP λmax values for the yellow cone class between Trinidad and Cumana guppies. Absence of the short-wave-shifted LWS-3 and the green-yellow cone in the green swordtail supports the hypothesis that this cell class of the guppy co-expresses the LWS-1 and LWS-3. These results reveal the basis of variability in the guppy visual system and provide insight into the behavior and ecology of these tropical fishes.

The high-yielding rice cultivar Takanari has fast photosynthetic induction owing to a high electron transport rate, stomatal conductance, and metabolic flux, leading to high daily carbon gain under fluctuating light.

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