Okihito Yano

Molecular phylogeny of Japanese Eleocharis (Cyperaceae) based on ITS sequence data, and chromosomal evolution

ITS sequence data were used to estimate the phylogeny of 24 Japanese Eleocharis species and to make karyomorphological observations on 19 of these taxa. Two major clades were identified in Japanese Eleocharis molecular phylogenetic trees: (1) one including all species of section Limnochloa, and (2) another comprising two sections, Pauciflorae and Eleocharis. Phylogenetic analysis including both Japanese and North American species also shows strong support for monophyly of the Mutatae/Limnochloa clade. The width of the spikelets in the species Mutatae/Limnochloa is the same as that of the culms, indicating that the relative widths of spikelets and culms are useful characteristics for classification. Two major clades were supported by karyomorphological data. All taxa of section Limnochloa had very small chromosomes, while sections Pauciflorae and Eleocharis had large chromosomes. The basic chromosome number of sections Eleocharis and Pauciflorae is thought to be x=5. Chromosomal evolution in the genus Eleocharis with diffuse centromeric chromosomes may be caused by both aneuploidization and polyploidization. Our data suggest that a 3-bp insertion near the 3′ end of the 5.8S gene is useful for intrageneric delimitations of the genus Eleocharis.

Phylogeography of the Japanese common sedge, Carex conica complex (Cyperaceae), based on chloroplast DNA sequence data and chromosomal variation.

UNLABELLED PREMISE OF THE STUDY Genetic and chromosomal variations in plants are often reflected in the geographical distribution patterns. Therefore, identifying such phylogeographical patterns on population is important for understanding the process of plant diversification and speciation, and analyzing both molecular and cytological aspects is necessary. • METHODS We investigated the phylogeographic pattern and genetic diversity of the widespread Japanese sedge, Carex conica complex, based on chloroplast DNA haplotypes and chromosomal variations. • KEY RESULTS Sixteen distinct haplotypes were detected from 258 individuals in the C. conica complex inferred from the cpDNA sequences of intergenic spacer (IGS) between atpB and rbcL, IGS between trnT and trnL, trnL intron, and IGS between trnL and trnF. Most haplotypes showed distinct geographical structures. Phylogenetic analyses revealed two major clades, clades I and II, among 16 haplotypes of the complex. The haplotypes of clade I were mainly found in eastern Japan, while most haplotypes of clade II were found in western Japan. Four intraspecific aneuploids of 2n = 32, 34, 36, and 38, with forming normal bivalents in meiotic divisions, were also found in the complex. The geographical distribution of these intraspecific aneuploids corresponded well with those of the haplotypes. • CONCLUSIONS Our results suggest that the genetic diversity and chromosomal variations in the C. conica complex may have originated from contractions and expansions of geographical ranges affected by Quaternary climatic oscillations.

Phylogeny of Najas (Hydrocharitaceae) revisited: Implications for systematics and evolution

Najas (Hydrocharitaceae) is a cosmopolitan genus of 30–40 species of aquatic plants. While an infrageneric subdivision into two subgenera is generally accepted, various sectional classifications proposed in subg. Caulinia have been controversial. Earlier analyses identified tropical Asia, which harbors more than one-third of all species, as the area of origin for the genus, but this inference requires re-evaluation using worldwide taxon sampling. Polyploidy has been widely observed in the genus but its correlation with phylogeny has yet to be explored. Here we applied a molecular phylogenetic approach using balanced taxon sampling (1) to test infrageneric classifications, (2) to re-assess biogeographic origin, and (3) to explore whether and how polyploidy characterizes evolutionary lineages. Our analyses of plastid and nuclear (ITS) DNA datasets produce largely congruent results that recover the two subgenera but find little support for most sectional classifications. To overcome this shortfall, we propose a new sectional classification of subg. Caulinia . The previously inferred tropical Asian origin of the genus is rejected and, instead, North America is discerned as the ancestral area, implicating dispersal of the most recent common ancestor of Najas and its sister genera in Hydrocharitaceae from tropical Asia. Based on chromosome counts confirmed in the present study and those compiled from literature, the role of polyploidization in the evolution of Najas is shown to be relatively limited, in contrast to the extreme infraspecific chromosome variation previously reported.

Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-Level Analysis of Public DNA Database Data

Abstract Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been sampled. Thus these studies typically do not make full use of the multigene datasets in public DNA databases to test species coherence and select optimal sequences to represent a species. In this study, we introduce a set of tools developed in the R programming language to construct individual-based trees from NCBI GenBank data and present a set of trees for the genus Carex (Cyperaceae) constructed using these methods. For the more than 770 species for which we found sequence data, our approach recovered an average of 1.85 gene regions per specimen, up to seven for some specimens, and more than 450 species represented by two or more specimens. Depending on the subset of genes analyzed, we found up to 42% of species monophyletic. We introduce a simple tree statistic—the Taxonomic Disparity Index (TDI)—to assist in curating specimen-level datasets and provide code for selecting maximally informative (or, conversely, minimally misleading) sequences as species exemplars. While tailored to the Carex dataset, the approach and code presented in this paper can readily be generalized to constructing individual-level trees from large amounts of data for any species group.

Phylogeny of Isolepis (Cyperaceae) revisited: non-monophyletic nature of I. fluitans sensu lato and resurrection of I. lenticularis

The aquatic and wetland ephemeral genus Isolepis (Cyperaceae) comprises 76 species mostly in the southern hemisphere, and especially Africa and Australasia. The latest taxonomic revision recognizes three subgenera (Fluitantes, Isolepis and Micranthae) and three sections in subgen. Isolepis. Subgen. Fluitantes, mat-forming perennial herbs typically bearing a single terminal spikelet, comprises nine species with a nearly cosmopolitan distribution except in Americas and Antarctica. Of these, I. fluitans includes infraspecific taxa from Africa–Europe and Asia–Australasia that are distinguished by the length of the involucral bract relative to the spikelet. This morphological character is also used in the key to subgen. Fluitantes that separates African–European and Asian–Australasian species. The overall morphological evidence conflicts with the species recognition of I. fluitans sensu lato and rather indicates the non-monophyly of I. fluitans, which we tested in a phylogenetic framework. Sequence data from three plastid DNA regions and nuclear ITS were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. We obtained moderately resolved phylogenies with the plastid DNA and ITS data sets. Although partially conflicting, both phylogenies rejected the monophyly of I. fluitans and instead revealed inter-continental pattern with infraspecific taxa showing close relationships with species in the subgenus within their geographic area. A revised key to species of subgenus Fluitantes is provided with the Asian–Australasian I. fluitans var. lenticularis resurrected to species rank as I. lenticularis. The phylogeny reveals a single dispersal event from Africa to Australasia, or vice versa in subgen. Fluitantes.

Molecular evidence for a natural hybrid between Isolepis crassiuscula and Isolepis lenticularis (Cyperaceae) in New Zealand

ABSTRACT Isolepis R.Br. (Cyperaceae) is a genus of aquatic, wetland, or ephemeral sedges that comprises 76 species, mostly in the southern hemisphere, especially Africa and Australasia. Isolepis crassiuscula Hook.f., Isolepis lenticularis R.Br. and Isolepis producta (C.B. Clarke) K.L.Wilson are among the Australasian members of a morphologically well-defined subgenus Fluitantes. Specimens belonging to this subgenus, collected from Mount Tongariro, New Zealand, showed ambiguous yet somewhat intermediate morphology compared with these three species. We sequenced directly, or cloned and sequenced, nuclear DNA (nrITS) and chloroplast DNA (rbcL, rps16 and trnL) regions of these collections and samples of the three aforementioned species of subgenus Fluitantes. Ribotypes and chloroplast haplotypes were compared to resolve if the Tongariro collection was of hybrid origin and, if so, to address which of the three species may have been involved in the hybridisation event. The Tongariro plants had the species-specific ribotypes of I. crassiuscula and I. lenticularis and the chloroplast haplotype of I. lenticularis, strongly suggesting hybrid origin between them. No data support the inclusion of I. producta as a parent. The morphologically uniform population from which the Tongariro plants were collected is likely to be derived from a single hybridisation event, although this hypothesis merits further investigation.