Oxytricha is a well‐known ciliate genus having a long, but convoluted taxonomic history, which aside from its non‐monophyly and subsequent dismembering into other genera, has a major issue: the type species O. granulifera is consistently paraphyletic. To understand their paraphyly in the context of our perception of species and genera according to the integrated taxonomy concept, we evaluated the phylogenetic status of differe...

Aphids are worldwide distributed pests, which feed on plant sap and cause serious losses to agricultural and forestry industries. Relatively few comprehensive studies have been conducted on aphid diversity in subtropics, although these regions may harbour hidden aphid diversity due to high plant diversity. In this study, we conducted DNA barcoding analysis for aphids in subtropical regions based on a comprehensive DNA barcode...

Evolutionary analysis of Prodiamesinae has long been impeded by lack of information, and its phylogenetic relationship with Orthocladiinae remains questionable. Here, ten complete mitochondrial genomes (mitogenomes) of Orthocladiinae sensu lato were newly sequenced, including three Prodiamesinae species and seven Orthocladiinae species. Coupled with published mitogenomes, a total of 12 mitogenomes of Orthocladiinae sensu lato...

Insects have invaded marine habitats only rarely and secondarily. Recently, we discovered a flightless dipteran species skating rapidly on the surface of seawater ponds at the Pacific coast of eastern China. Morphological analyses initially suggested an isolated position of the non‐biting midge, suggesting the erection of a new genus within Chironomini (Diptera: Chironomidae). However, an analysis of molecular data revealed th...

Climate changes can have fundamental impacts on the distributional patterns of montane species, and range shifts frequently lead to allopatric divergence followed by the establishment of secondary contact zones. Many European and North American organisms have retreated to southern refugia during glacial periods and colonized northward during postglacial periods, but little is known about the evolutionary response of cold‐adapt...

Rhinolophids (horseshoe bats) are a widespread and diverse family. Their high level of morphological convergence has made taxonomic identification and estimation of species diversity problematic. The Rhinolophus philippinensis group, which is characterized with huge ears and low echolocation frequency relative to body size, is a specific group among all the rhinolophid groups, but the phylogeny of this group is poorly understo...

Deserts and arid regions are perceived to have low biological and genetic diversity, which has partially influenced the identification of psammophilic species, especially taxonomic inferences based on morphology alone. Recent studies of Dipus sagitta have revealed clear, deep genetic divergence beyond the species level within this monotypic genus. To clarify the taxonomy of Dipus , we examined a morphometric dataset consisting...

Polypedilum Kieffer (Diptera: Chironomidae), with 520 currently known species worldwide, can be extremely difficult to identify species level based on the morphology. We used 3,670 cytochrome c oxidase subunit I (COI) barcodes to explore the efficiency of the COI barcodes to differentiate between species in a superdiverse aquatic insect genus. The Barcode of Life Data System (BOLD) presented 286 BIN clusters in Polypedilum , r...

Over the past decade, molecular approaches to species delimitation have seen rapid development. However, species delimitation based on a single locus, for example, DNA barcodes, can lead to inaccurate results in cases of recent speciation and incomplete lineage sorting. Here, we compare the performance of Automatic Barcode Gap Discovery ( ABGD ), Bayesian Poisson tree processes ( PTP ), networks, generalized mixed Yule coalesc...

A high diversity of pleurostomatid ciliates has been discovered in the last decade, and their systematics needs to be improved in the light of new findings concerning their morphology and molecular phylogeny. In this work, a new genus, Protolitonotus gen. n., and two new species, Protolitonotus magnus sp. n. and Protolitonotus longus sp. n., were studied. Furthermore, 19 novel nucleotide sequences of SSU rDNA , LSU rDNA and IT...

The white‐bellied rat, Niviventer , is a genus endemic to Southeast Asia and China. However, the interspecific phylogenetic relationships and species diversity of this genus remain poorly understood. In the present study, single and multi‐locus analyses were performed. Phylogenetic reconstruction on Cytochrome b (512 individuals, including data from Genbank) revealed five major clades with approximately 35 operational taxonomi...

Pareatidae are a group of mollusc‐eating snakes widely distributed in S outh‐eastern A sia. Due to their dietary specialization, the asymmetric dentition of pareatids has recently become an interesting issue in evolutionary biology. However, phylogenetic relationships and species diversity of pareatids are still poorly studied. A total of three P areas species, P . formosanus ( V an D enburgh 1909), P . compressus ( O shima 19...

Liu, W., Yi, Z., Lin, X., Warren, A. & Song, W. (2012). Phylogeny of three choreotrich genera (Protozoa, Ciliophora, Spirotrichea), with morphological, morphogenetic and molecular investigations on three strobilidiid species. — Zoologica Scripta , 41 , 417–434. The phylogenetic relationships among three strobilidiid genera, namely Strobilidium , Rimostrombidium and Pelagostrobilidium , are investigated using a combination of m...

Wu, H.‐C., Lin, R.‐C., Hung, H.‐Y., Yeh, C.‐F., Chu, J.‐H., Yang, X.‐J., Yao, C.‐J., Zou, F.‐S., Yao, C.‐T., Li, S.‐H. & Lei, F.‐M. (2011). Molecular and morphological evidences reveal a cryptic species in the Vinaceous Rosefinch Carpodacus vinaceus (Fringillidae; Aves). — Zoologica Scripta, 40 , 468–478. The Vinaceous Rosefinch ( Carpodacus vinaceus ) is endemic in East Asia with two recognized subspecies – C. v. vinaceus , d...

Lin, C.‐J., Lin, H.‐D., Wang, J.‐P., Chao, S.‐C. & Chiang, T.‐Y. (2007). Phylogeography of Hemibarbus labeo (Cyprinidae): secondary contact of ancient lineages of mtDNA. — Zoologica Scripta, 39 , 23–35. Nucleotide sequences of the D‐loop control region of mtDNA were used to assess the genetic structure and phylogeography of Hemibarbus labeo in Mainland China and Taiwan. A hierarchical analysis of molecular variance of populati...

The morphology‐based phylogeny of freshwater eels, proposed by V. Ege in 1939, has been accepted as the basis of eel classification since that time. However, this has been called into question by recent molecular studies. Most of the morphological characteristics recognized by Ege are morphometric. Since methods for the application of morphometric data to phylogeny construction have not been fully established, it is unclear wh...