Ludwigia (Onagraceae) is a worldwide wetland genus with 83 species currently classified as members of 23 sec­ tions. Past studies have documented the morphological diversity and complex evolutionary history. Here we provide the first comprehensive molecular phylogeny of Ludwigia, using our new data to examine the existing evolutionary hypotheses. We employed both nuclear (ITS, waxy) and chloroplast (rps16, rpl16, trnL‐trnF, trnL‐CD, trnG) DNA regions for this study. Our results suggest that the North Temperate haplostemonous (NTH) group and a second group that includes all other species of Ludwigia(clade B) form strongly supported sister clades. In the NTH group, a monophyletic sect. Ludwigia is sister to the Microcarpium complex, but sect. Microcarpium and sect. Isnardia are not monophyletic. In clade B, the multi‐species sec­ tions Jussiaea and Macrocarpon are well‐supported monophyletic clades, but others, including the largest sect. Myrtocarpus, are not monophyletic. In sum, this first molecular phylogeny of Ludwigia clarifies and supports several major relationships in the genus but also highlights parts of the classification that should be changed. Our results imply that allopolyploidy played an important role in the evolutionary history of the genus, giving rise to complex patterns of relationships that are not yet adequately reflected in the classification.

Species identification based on the DNA sequence of a fragment of the cytochrome c oxidase subunit I gene in the mitochondrial genome, DNA barcoding, is widely applied to assist in sustainable exploitation of fish resources and the protection of fish biodiversity. The aim of this study was to establish a reliable barcoding reference database of the native ray-finned fishes in Taiwan. A total of 2993 individuals, belonging to 1245 species within 637 genera, 184 families and 29 orders of ray-finned fishes and representing approximately 40% of the recorded ray-finned fishes in Taiwan, were PCR amplified at the barcode region and bidirectionally sequenced. The mean length of the 2993 barcodes is 549 bp. Mean congeneric K2P distance (15.24%) is approximately 10-fold higher than the mean conspecific one (1.51%), but approximately 1.4-fold less than the mean genetic distance between families (20.80%). The Barcode Index Number (BIN) discordance report shows that 2993 specimens represent 1275 BINs and, among them, 86 BINs are singletons, 570 BINs are taxonomically concordant, and the other 619 BINs are taxonomically discordant. Barcode gap analysis also revealed that more than 90% of the collected fishes in this study can be discriminated by DNA barcoding. Overall, the barcoding reference database established by this study reveals the need for taxonomic revisions and voucher specimen rechecks, in addition to assisting in the management of Taiwan's fish resources and diversity.

While it is known that whole genome duplication (WGD) and reticulate evolution play important roles in plant evolution, the origins and evolutionary histories of most polyploid and reticulate groups are still poorly known. The North Temperate haplostemonous (NTH) Ludwigia L. (sections Isnardia (L.) W. L. Wagner & Hoch, Ludwigia, Microcarpium Munz, and Miquelia P. H. Raven) group, characterized by having 4-merous and haplostemonous flowers, pluriseriate and free seeds, glabrous and convex nectaries, and a north-temperate distribution, is a polyploid complex (2×, 4×, 6×, and 8×) of 24 species with frequent reports of inter- and intrasectional hybridization. Although earlier biosystematics studies postulated some evolutionary scenarios and recent molecular phylogenetic studies have partially tested these propositions, the full history of their reticulate evolution remains puzzling. In this study, we sequenced four chloroplast regions (rpL16, rpoB-trnC, trnL-trnF, and ycf6-psbM) and conducted extensive molecular cloning of the biparentally inherited single-copy nuclear PgiC gene (376 clones in total), sampling 23 of the 24 NTH Ludwigia species whose chromosome numbers and ploidy levels were confirmed. Both the chloroplast and PgiC trees include strongly supported sister clades of section Ludwigia (four diploid species) and the “Microcarpium complex” (composed of sections Isnardia, Microcarpium, and Miquelia), which together are sister to the rest of Ludwigia. In the PgiC tree, eight clades are identified within the Microcarpium complex, with four clades including no extant diploid species. Neither sections Isnardia nor Microcarpium are monophyletic, while the monospecific section Miquelia has a hybrid origin. By integrating our phylogenetic trees with previous cytological hypotheses, the reticulate evolution of NTH Ludwigia is disentangled and four to eight extinct diploid species are inferred. Ancestral area reconstruction supports a North American origin of L. ovalis whose current East Asian distribution reflects a relict of the Arcto-Tertiary Geoflora. Based on our results, we propose to synonymize sections Microcarpium and Miquelia under the expanded section Isnardia.

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