The Arctic Warbler Phylloscopus borealis– three anciently separated cryptic species revealed

The Arctic Warbler Phylloscopus borealis breeds across the northern Palaearctic and northwestern‐most Nearctic, from northern Scandinavia to Alaska, extending south to southern Japan, and winters in Southeast Asia, the Philippines and Indonesia. Several subspecies have been described based on subtle morphological characteristics, although the taxonomy varies considerably among different authors. A recent study (T. Saitoh et al. (2010) BMC Evol. Biol. 10 : 35) identified three main mitochondrial DNA clades, corresponding to: (1) continental Eurasia and Alaska, (2) south Kamchatka, Sakhalin and northeast Hokkaido, and (3) most of Japan (Honshu, Shikoku, Kyushu). These three clades were estimated to have diverged during the late Pliocene to early Pleistocene (border at c. 2.6 million years ago). Differences in morphometrics have also been reported among members of the three clades (T. Saitoh et al. (2008) Ornithol. Sci. 7 : 135–142). Here we analyse songs and calls from throughout the range of the Arctic Warbler, and conclude that these differ markedly and consistently among the populations representing the three mitochondrial clades. Kurile populations, for which no sequence data are available, are shown to belong to the second clade. To determine the correct application of available scientific names, mitochondrial DNA was sequenced from three name‐bearing type specimens collected on migration or in the winter quarters. Based on the congruent variation in mitochondrial DNA, morphology and vocalizations, we propose that three species be recognized: Arctic Warbler Phylloscopus borealis (sensu stricto) (continental Eurasia and Alaska), Kamchatka Leaf Warbler Phylloscopus examinandus (Kamchatka (at least the southern part), Sakhalin, Hokkaido and Kurile Islands), and Japanese Leaf Warbler Phylloscopus xanthodryas (Japan except Hokkaido).     

Multilocus phylogeny and species delimitation within the genus Glauconycteris (Chiroptera,Vespertilionidae), with the description of a new bat species from the Tshopo Province of the Democratic Republic of the Congo

The genus Glauconycteris Dobson, 1875 currently contains 12 species of butterfly bats, all endemic to sub‐Saharan Africa. Most species are rarely recorded, with half of the species known from less than six geographic localities. The taxonomic status of several species remains problematic. Here, we studied the systematics of butterfly bats using both morphological and molecular approaches. We examined 45 adult specimens for external anatomy and skull morphology, and investigated the phylogeny of Glauconycteris using DNA sequences from three mitochondrial genes and 116 individuals, which in addition to outgroup taxa, included nine of the twelve butterfly bat species currently recognized. Four additional nuclear genes were sequenced on a reduced sample of 69 individuals, covering the outgroup and Glauconycteris species. Our molecular results show that the genus Glauconycteris is monophyletic, and that it is the sister‐group of the Asian genus Hesperoptenus. Molecular dating estimates based on either Cytb or RAG2 data sets suggest that the ancestor of Glauconycteris migrated into Africa from Asia during the Tortonian age of the Late Miocene (11.6–7.2 Mya), while the basal diversification of the crown group occurred in Africa at around 6 ± 2 Mya. The species G. superba is found to be the sister‐group of G. variegata, questioning its placement in the recently described genus Niumbaha. The small species living in tropical rainforests constitute a robust clade, which contains three divergent lineages: (i) the “poensis” group, which is composed of G. poensis, G. alboguttata, G. argentata, and G. egeria; (ii) the “beatrix” group, which contains G. beatrix and G. curryae; and (iii) the “humeralis” group, which includes G. humeralis and a new species described herein. In the “poensis” group, G. egeria is found to be monophyletic in the nuclear tree, but polyphyletic in the mitochondrial tree. The reasons for this mito‐nuclear discordance are discussed.     

Descriptions of two new species of the botiid genus Leptobotia Bleeker, 1870 (Teleostei: Cypriniformes) from South China

Two new species of Leptobotia are here described as L. rotundilobus from the Xin'an-Jiang of the upper Qiantang-Jiang basin in both Anhui and Zhejiang Provinces and the Cao'e-Jiang in Zhejiang Province, and L. paucipinna from the Qing-Jiang of the middle Chang-Jiang basin in Hubei Province, South China. Both have a plain brown body as found in L. bellacauda Bohlen & Šlechtová, 2016, L. microphthalma Fu & Ye, 1983, L. posterodorsalis Chen & Lan, 1992 and L. tientainensis (Wu, 1930). The two new species are distinct from these species in vertebral counts, further from L. posterodorsalis in vent placement and further from the other three species in pectoral-fin length. Both differ in caudal-fin coloration and shape, and dorsal-fin location and coloration, and also in internal morphology. Their validity is confirmed by their own monophyly recovered in a phylogenetic analysis based on the mitochondrial cyt b and COI genes.     

Taxonomy and phylogeny of Lineus torquatus and allies (Nemertea,Lineidae) with descriptions of a new genus and a new cryptic species

The heteronemertean genus Lineus Sowerby, 1806 has been badly in need of revision because of its apparent non-monophyly. In this paper, we focus on Lineus torquatus Coe, 1901, one of the heteronemertean species that occur commonly in waters around the North Pacific, as well as a few other allied species distributed in the western North Pacific, including Lineus alborostratus Takakura, 1898 and Cerebratulus montgomeryi Coe, 1901. Based on phylogenetic analyses using 16S, COI, 28S, 18S, and H3 gene and ITS sequences, we detected a well-supported clade comprised of heteronemerteans with a frontal white band on the head, to which we add Kulikovia gen. nov. This genus is nested within a more comprehensive, highly supported clade, here named the Siphonenteron-clade, which contains Tenuilineus bicolour (Verrill, 1892), Lineus flavescens Coe, 1905, Siphonenteron bilineatum (Renier, 1804), S. cf. bilineatum, Lineus cf. caputornatus, and Lineus sp. from Guam. Our analyses confirmed the presence of a cryptic species of what was formerly known as the cherry-red and reddish forms of Lineus torquatus, herein described as Kulikovia manchenkoi sp. nov. based on some external characters, internal morphology, and the four genetic markers (COI, 16S, H3, and ITS). In contrast to the species pair K. torquata–K. manchenkoi, the reddish form of K. alborostrata does not differ genetically from the typical form of this species. The significance of the external and internal characters for distinguishing cryptic species is discussed.

http://zoobank.org/urn:lsid:zoobank.org:pub:9BECBC60-9C82-48EC-AD36-FC564D82A5BChttp://zoobank.org/urn:lsid:zoobank.org:act:D02B2339-4F65-4517-9B13-DD4AAB0C55C5http://zoobank.org/urn:lsid:zoobank.org:act:8D239B62-E655-4721-90F0-A4944DD8A3C7     

A review of the genus Strophidon (Anguilliformes: Muraenidae), with description of a new species

Strophidon McClelland is a muraenid genus with characteristic appearance of a very elongated body, a large mouth cleft and anteriorly placed eyes. The nomenclature and taxonomic history of species within Strophidon are contentious and its members are easily misidentified. In the present study, species of the genus Strophidon are revised based on morphological and molecular data, and five species are considered valid, including S. dawydoffi Prokofiev, S. dorsalis (Seale), S. sathete (Hamilton), S. ui Tanaka and a new species, S. tetraporus. Strophidon tetraporus sp. nov. is described based on 15 specimens from Indonesia, the Philippines, Taiwan and Vietnam with the unique characteristic of the constant presence of the fourth infraorbital pore among species of Strophidon. The intraspecific variation of vertebral formula within S. dorsalis is discussed based on molecular data. Muraena macrurus Bleeker and Thyrsoidea longissima Kaup are synonyms of S. sathete that can be distinguished from the most similar congener S. ui by a longer tail, smaller eyes and more inner maxillary and inner dentary teeth. A key to identify species of Strophidon is provided. The distribution and maximum size of each species are also re-evaluated.     

A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico

Hybrid speciation may contribute significantly to generating biodiversity, but only a few well‐documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hallmarks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (Xiphophorus hellerii and Xiphophorus maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here, we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X. clemenciae– the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X. clemenciae appears to be rather ancient, and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, because they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X. clemenciae. The population structure within these species shows an isolation‐by‐distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X. clemenciae and X. helleriii and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X. clemenciae.     

Molecular phylogenetic analysis of the Amiota apodemata and Amiota sinuata species groups (Diptera: Drosophilidae), with descriptions of four new species

The phylogenetic relationships among the East Asian species of the apodemata and sinuata species groups of the genus Amiota were investigated based on DNA sequences of the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. A total of 23 samples of 12 species were employed as in‐group taxa, and one sample for each of four other Amiota species were used as out‐groups. The results suggested with strong confidence the monophyly of both the apodemata and the sinuata groups, whereas the monophyly of the ‘apodemata group + sinuata group’ cluster was less supported. Based on its geographical distribution, the origin of the sinuata group is supposed to be southern China. Four new species were described from Guangxi and Yunnan, China: Amiota reikae Xu & Chen sp. nov. , Amiota guiensis Xu & Chen sp. nov. , Amiota hesongensis Xu & Chen sp. nov. , and Amiota polytreta Xu & Chen sp. nov. © 2013 The Linnean Society of London     

Phylogeny and species delimitation of the C-genome diploid species in Oryza

The diploid Oryza species with C-genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C-genome (BBCC,CCDD).Despite extensive studies,the phylogenetic relationship among the C-genome species and the taxonomic status of some taxa remain controversial.In this study,we reconstructed the phylogeny of three diploid species with C-genome (Oryza officinalis,O.rhizomatis,and O.eichingeri) based on sequences of 68 nuclear single-copy genes.We obtained a fully resolved phylogenetic tree,clearly indicating the sister relationship of O.officinalis and O.rhizomatis,with O.eichingeri being the more divergent lineage.Incongruent phylogenies of the C-genome species found in previous studies might result from lineage sorting,introgression/hybridization and limited number of genetic markers used.We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O.eichingeri.Analyses of two datasets (68 genes with a single sample,and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O.eichingeri.In addition,we evaluated the impact of the number of sampled individuals and loci on species delimitation.Our simulation suggests that sampling multiple individuals is critically important for species delimitation,particularly for closely related species.     

拟棘壳孢属的一新种及本属已知种的检索表

本文报道分离自贵州省土壤的拟棘壳孢属Pyrenochaetopsis真菌一新种,对该种结合形态特征及分子系统学分析明确其分类地位,命名为土栖拟棘壳孢Pyrenochaetopsis terricola;编制了该属13个已知种的分种检索表。研究标本保存于贵州大学植物病理学实验室（HGUP）和中国微生物菌种保藏管理委员会普通微生物中心（CGMCC）。     

指定木霉属三个种的附加模式并报道中国新记录种

对来自我国南方的木霉属标本进行分类学研究,首次发现灵芝木霉T. ganodermatis、异味木霉T. ingratum 和特里克木霉T. trixiae的有性阶段,对它们进行描述并指定3个种的附加模式。报道了3个中国新记录种：新厚木霉Trichoderma neocrassum、垫状木霉T. pulvinatum和塞缪尔斯木霉T. samuelsii、提供了它们的形态描述和图示。基于RPB2和TEF1基因序列的系统发育分析确定了上述种的系统发育位置。建立一个新名称取代晚出同名Trichoderma crystalligenum W.T. Qin & W.Y. Zhuang。     

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

Abstract The diploid Oryza species with C‐genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C‐genome (BBCC, CCDD). Despite extensive studies, the phylogenetic relationship among the C‐genome species and the taxonomic status of some taxa remain controversial. In this study, we reconstructed the phylogeny of three diploid species with C‐genome (Oryza officinalis, O. rhizomatis, and O. eichingeri) based on sequences of 68 nuclear single‐copy genes. We obtained a fully resolved phylogenetic tree, clearly indicating the sister relationship of O. officinalis and O. rhizomatis, with O. eichingeri being the more divergent lineage. Incongruent phylogenies of the C‐genome species found in previous studies might result from lineage sorting, introgression/hybridization and limited number of genetic markers used. We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O. eichingeri. Analyses of two datasets (68 genes with a single sample, and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O. eichingeri. In addition, we evaluated the impact of the number of sampled individuals and loci on species delimitation. Our simulation suggests that sampling multiple individuals is critically important for species delimitation, particularly for closely related species.     

A new genus and species of octocoral with aragonite calcium-carbonate skeleton (Octocorallia,Helioporacea) from Okinawa,Japan

A new genus and species of octocoral with a calcium-carbonate skeleton, Nanipora kamurai sp. n., is described from a shallow coral reef in Okinawa, Japan. Contrary to most octocorals, the skeleton is composed of crystalline aragonite as in blue coral Heliopora. The results of molecular phylogenetic analyses of sequences of mtMutS, COI, and ITS1-5.8s-ITS2-28S region suggest Nanipora gen. n. specimens should be included in order Helioporacea. Based on morphological results compared with other Helioporacea including the genus Epiphaxum (family Lithotelestidae), we establish the new genus Nanipora within Lithotelestidae. This is the first time that a close molecular phylogenetic relationship between Heliopora and a related genus within Helioporacea has been revealed.     

Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex

The well-documented Floridian 'Gulf/Atlantic' marine genetic disjunction provides an influential example of vicariant cladogenesis along a continental coastline for major elements of a diverse nearshore fauna. We are engaged in a two-part study that aims to place this disjunction into a regional Caribbean Basin phylogenetic perspective using the scorched mussel Brachidontes exustus as an exemplar. Our first step, documented here, is to thoroughly characterize the genetic structure of Floridian scorched mussel populations using mitochondrial (mt) and nuclear markers. Both sets of markers recovered the expected disjunction involving sister clades distributed on alternate flanks of peninsular Florida and lineage-specific mt molecular clocks placed its origin in the Pliocene. The two sister clades had distinct population genetic profiles and the Atlantic clade appears to have experienced an evolutionarily recent bottleneck, although plots of the relative estimates of N through time are consistent with its local persistence through the last Ice Age Maximum. Our primary novel result, however, was the discovery that the Gulf/Atlantic disjunction represents but one of three cryptic, nested genetic discontinuities represented in Floridian scorched mussel populations. The most pronounced phylogenetic split distinguished the Gulf and Atlantic sister clades from two additional nested cryptic sister clades present in samples taken from the southern Florida tropical marine zone. Floridian populations of B. exustus are composed of four cryptic taxa, a result consistent with the hypothesis that the Gulf/Atlantic disjunction in this morphospecies is but one of multiple latent regional genetic breakpoints.