Description of a new species of marine amoeba Korotnevella mutabilis n. sp. (Amoebozoa,Dactylopodida)

Korotnevella (Amoebozoa, Dactylopodida) is a genus of naked lobose amoebae with a dactylopodial morphotype. The cell membrane of these amoebae is covered with a monolayer of scales. The structure and size of scales are considered as species-specific features. Here, we describe a new marine species, Korotnevella mutabilis n. sp., isolated from the bottom sediment sample of Nivå Bay (Baltic Sea, The Sound) and studied with light and electron microscopy as well as with molecular phylogenetic analysis. This species has a number of morphological similarities with Korotnevella monacantholepis, such as size of the cell, L/B ratio, the nucleus structure and the type of a biotope from which both species were isolated. At the same time, Korotnevella mutabilis n. sp. differs from K. monacantholepis in the structure of basket-shaped scales: Korotnevella mutabilis n. sp. has an enclosed hammock-shaped latticework basket and up to two spines while K. monacantholepis has an opened two-row latticework basket and never has two spines. According to molecular phylogenetic analyses based on the sequences of the mitochondrial COI gene, Korotnevella mutabilis n. sp. is a distinct species, highly divergent from other Korotnevella species.     

Cochliopodium arabianum n. sp. (Amorphea,Amoebozoa)

A new species of Cochliopodium isolated from freshwater at Arabia Lake in Lithonia, GA, USA is described based on light microscopic morphology, fine structure, and molecular genetic evidence. Cochliopodium arabianum n. sp., previously labeled as “isolate Con1” in prior publications, has been shown to group within the genus Cochliopodium in our molecular phylogenetic analysis. Light microscopy and fine structure evidence indicates the new isolate not only shares characters of the genus but also unique distinctive features. Cochliopodium arabianum n. sp. is typically round when stationary; or oval to sometimes broadly flabellate or triangular in shape during locomotion, with average length of 35 μm and breadth of 51 μm. Fine structure evidence indicates C. arabianum n. sp. has tower‐like scales, lacking a terminal spine, sharing high similarity with its closest relative C. actinophorum. However, the scales of C. arabianum n. sp. are unique in height and the breadth of the base plate. Both morphological and molecular data, including SSU‐rDNA and COI, indicate that this new species falls in a clade sufficiently different from other species to suggest that it is a valid new species.     

Three New Freshwater Cochliopodium Species (Himatismenida,Amoebozoa) from the Southeastern United States

Cochliopodium is a lens‐shaped genus of Amoebozoa characterized by a flexible layer of microscopic dorsal scales. Recent taxonomic and molecular studies reported cryptic diversity in this group and suggested that the often‐used scale morphology is not a reliable character for species delineation in the genus. Here, we described three freshwater Cochliopodium spp. from the southeastern United States based on morphological, immunocytochemistry (ICC), and molecular data. A maximum‐likelihood phylogenetic analysis and pairwise comparison of COI sequences of Cochliopodium species showed that each of these monoclonal cultures were genetically distinct from each other and any described species with molecular data. Two of the new isolates, “crystal UK‐YT2” (Cochliopodium crystalli n. sp.) and “crystal‐like UK‐YT3” (C. jaguari n. sp.), formed a clade with C. larifeili, which all share a prominent microtubule organizing center (MTOC) and have cubical‐shaped crystals. The “Marrs Spring UK‐YT4” isolate, C. marrii n. sp., was 100% identical to “Cochliopodium sp. SG‐2014 KJ569724 .” These sequences formed a clade with C. actinophorum and C. arabianum. While the new isolates can be separated morphologically, most of the taxonomic features used in the group show plasticity; therefore, Cochliopodium species can only be reliably identified with the help of molecular data.     

Cryptic speciation in the narrow‐headed vole Lasiopodomys (Stenocranius) gregalis (Rodentia: Cricetidae)

Recent study on Lasiopodomys (Stenocranius) gregalis has revealed four clear mitochondrial lineages with differences exceeding the species level. The most divergent is the clade from south‐eastern Transbaikalia. Multilocus (six nuclear genes), morphological (dental characters of m1 and M3) and behavioural (breeding experiments) analyses were conducted to test the hypothesis that L. gregalis is a complex of two cryptic species. All of the applied methods distinguish the independent status of voles from south‐eastern Transbaikalia. This clade occupies a portion of the distribution range of the currently valid subspecies L. g. raddei including its terra typica. According to the results of cyt b analysis, the lectotype of L. g. raddei belongs to the Transbaikal clade. We re‐establish the species status for the taxon Lasiopodomys raddei including populations from south‐eastern Transbaikalia, as a cryptic species of the narrow‐headed vole complex.     

Korotnevella hemistylolepis n. sp. and Korotnevella monacantholepis n. sp. (Paramoebidae), two new scale-covered mesohaline amoebae

Two new species of Korotnevella Goodkov, 1988, Korotnevella hemistylolepis n. sp. and Korotnevella monacantholepis n. sp., are described from mesohaline ecosystems. The amoebae are characterized on the basis of light and electron microscopy with special emphasis on the structure of the basket scales, which have species-specific architecture. The two new species are the second and third ones recovered from environments other than freshwater. In terms of scale morphology they most closely resemble a freshwater species, Korotnevella bulla (Schaeffer, 1926) Goodkov, 1988. Two genus names, Dactylamoeba Korotnev, 1880 and Korotnevella Goodkov, 1988, are in current use. The latter name is preferred, pending rediscovery and characterization of Dactylamoeba elongata Korotnev, 1880, the type species of the genus. Korotnevella species can be divided into three groups on the basis of scale morphology, suggesting that the genus may not be monophyletic. A key to species is provided.     

A New Freshwater Amoeba: Cochliopodium pentatrifurcatum n. sp. (Amoebozoa,Amorphea)

Cochliopodium pentatrifurcatum n. sp. (ATCC^© 30935^TM) is described based on light microscopic morphology, fine structure, and molecular genetic evidence. Cochliopodium pentatrifurcatum n. sp. (length ~ 25 μm) is characterized by surface microscales (0.3 μm tall) containing a circular porous base (~ 0.6 μm diam.) with a thin peripheral rim. Five radially arranged feet, emanating from the base, support a short central column terminating apically as a funnel‐shaped collar (~ 0.5 μm diam.) composed of five radial, trifurcate rays extending from the center toward a thin peripheral rim. The central spine is 0.5–0.6 μm long. The comparative morphologies and combined molecular genetic evidence, SSU‐rDNA and COI, indicate that the new species falls in a clade sufficiently different from other species to suggest that it is a valid new species.     

A New Species of Centrohelid Heliozoan Acanthocystis amura n. sp. Isolated From Two Remote Locations in Russia

A new species of centrohelid heliozoan Acanthocystis amura from the Amur River, the Far East of Russia was studied with light‐ and electron microscopy. Acanthocystis amura has simple oval plate scales (1.2–2.6 × 1.0–1.8 μm) with an axial thickening and a thin border as well as two types of spine scales. The spine scales of type 1 were 1.3–4.8 μm long and had four small hooks on their tips. The spine scales of type 2 were shorter, 1.0–3.6 μm long and had four teeth at the distal end. The morphology of A. amura resembles that of Acanthocystis quadrifurca. They both have similar spine scales but their plate scales are completely different. Acanthocystis valdiviense differs from the new species in absence of hook‐bearing scales. Molecular phylogeny based on 18S rDNA consistently placed A. amura into Acanthocystis nichollsi/Acanthocystis costata clade, but relationships between those three species were not resolved. Morphology of another centrohelid strain from another location (the South Urals) has been compared with that of the original strain and few minor differences in size characteristics of the scales have been revealed.     

A New Heterotrophic Cryptomonad: Hemiarma marina n. g., n. sp.

We report a new heterotrophic cryptomonad Hemiarma marina n. g., n. sp. that was collected from a seaweed sample from the Republic of Palau. In our molecular phylogenetic analyses using the small subunit ribosomal RNA gene, H. marina formed a clade with two marine environmental sequences, and the clade was placed as a sister lineage of the freshwater cryptomonad environmental clade CRY1. Alternatively, in the concatenated large and small subunit ribosomal RNA gene phylogeny, H. marina was placed as a sister lineage of Goniomonas. Light and electron microscopic observations showed that H. marina shares several ultrastructural features with cryptomonads, such as flattened mitochondrial cristae, a periplast cell covering, and ejectisomes that consist of two coiled ribbon structures. On the other hand, H. marina exhibited unique behaviors, such as attaching to substrates with its posterior flagellum and displaying a jumping motion. H. marina also had unique periplast arrangement and flagellar transitional region. On the basis of both molecular and morphological information, we concluded that H. marina should be treated as new genus and species of cryptomonads.     

Isolation of polymorphic microsatellite loci in the clear lake gnat and two other phantom midge species of the genus Chaoborus (Diptera: Chaoboridae)

Chaoborus is of great interest to many freshwater ecologists. The adults can become pests in certain areas in North America and the larvae are an important food source for fish. In this preliminary study, we identified variable microsatellite loci in three species: Chaoborus astictopus (H_E = 0.52–0.76), Chaoborus americanus (H_E = 0.46–0.80) and Chaoborus punctipennis (H_E = 0.66–0.81). Using a biotin/streptavidin capture technique of repetitive sequences in a 96‐well format, we obtained microsatellite‐enriched genomic libraries for all three species and identified six polymorphic microsatellite markers for each species. None of the primers did yield a polymerase chain reaction fragment in a cross‐species test.     

Characterization of the LTR retrotransposon repertoire of a plant clade of six diploid and one tetraploid species

Comparisons of closely related species are needed to understand the fine‐scale dynamics of retrotransposon evolution in flowering plants. Towards this goal, we classified the long terminal repeat (LTR) retrotransposons from six diploid and one tetraploid species of Orobanchaceae. The study species are the autotrophic, non‐parasitic Lindenbergia philippensis (as an out‐group) and six closely related holoparasitic species of Orobanche [O. crenata, O. cumana, O. gracilis (tetraploid) and O. pancicii] and Phelipanche (P. lavandulacea and P. ramosa). All major plant LTR retrotransposon clades could be identified, and appear to be inherited from a common ancestor. Species of Orobanche, but not Phelipanche, are enriched in Ty3/Gypsy retrotransposons due to a diversification of elements, especially chromoviruses. This is particularly striking in O. gracilis, where tetraploidization seems to have contributed to the Ty3/Gypsy enrichment and led to the emergence of seven large species‐specific families of chromoviruses. The preferential insertion of chromoviruses in heterochromatin via their chromodomains might have favored their diversification and enrichment. Our phylogenetic analyses of LTR retrotransposons from Orobanchaceae also revealed that the Bianca clade of Ty1/Copia and the SMART‐related elements are much more widely distributed among angiosperms than previously known.     

<Emphasis Type="Italic">Prorocentrum rivalis</Emphasis> sp. nov. (Dinophyceae) and its phylogenetic affinities inferred from analysis of a mixed morphological and LSU rRNA data set

A new freshwater epiphytic Prorocentrum species, Prorocentrum rivalis, from the temperate region of the Haute-Vienne, France, is described. This species is the third freshwater species identified among approximately 60 marine Prorocentrum species. This new species is described using scanning electron microscope and phylogenetic analyses by a polyphasic approach (LSU rRNA sequences combined with 9 morphological characters). The phylogenetic analysis attests that P. rivalis is close to other planktonic freshwater species and the freshwater Prorocentrum clade is evolutionarily derived from an epiphytic freshwater prorocentroid ancestor. The unique marine species in the freshwater clade results from an ecophysiological reversion. P. rivalis differs from other epiphytic taxa by its rarity, its temperate distribution and its ecophysiological needs. The phylogeny confirms also that all planktonic Prorocentrum species are evolutionarily derived from epiphytic/benthic ancestors.     

Genetic structure of a morphological species within the amoeba genus Korotnevella (Amoebozoa: Discosea), revealed by the analysis of two genes

Amoebae of the genus Korotnevella are covered with scales, the structure of which is believed to be species–specific and allows distinguishing species reliably at the morphological level. We studied members of this genus in order to assess the genetic structure of the local populations of amoebae. For the present study we isolated nine freshwater strains of Korotnevella, belonging to three species, from two locations in North-Western Russia. In order to obtain data on the population structure of these amoebae, we identified all isolates based on the light-microscopic morphology and scale structure and investigated both inter-strain and intra-strain polymorphism of Cox I and 18S rRNA genes. Results show that both genes provide congruent patterns of population structure. The Cox I gene appears to be more reliable DNA barcode while the 18S rRNA gene shows an interesting pattern of polymorphism, which may represent phylotypes of amoebae. Local population of amoebae in every studied species consists of a number of genetic lineages (phylotypes), some shared between the populations while others are unique to a local habitat.     

Diversity of the snail‐eating snakes Pareas (Serpentes,Pareatidae) from Taiwan

Pareatidae are a group of mollusc‐eating snakes widely distributed in South‐eastern Asia. 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 Pareas species, P. formosanus (Van Denburgh 1909), P. compressus (Oshima 1910) and P. komaii (Maki 1931), have been reported for Taiwan. However, only P. formosanus is currently regarded as a valid species. Using mitochondrial sequence phylogeny, nuclear c‐mos haplotype network, as well as multivariate morphometrics, we re‐evaluated the taxonomic status of Pareas from Taiwan, the Ryukyus and adjacent regions. These lines of evidence showed congruent results for the coexistence of three Pareas species in Taiwan, with prominent genetic and morphological differentiation and differing level of dentition asymmetry. The currently used name P. formosanus should be applied only to the snakes with red iris, comparatively short lower jaw and totally smooth dorsal scales. An examination of the type material indicated that the name P. compressus should be regarded as a junior synonym of P. formosensis sensu stricto. Pareas komaii (Oshima 1910) is confirmed as a valid taxon with yellow iris, elongated lower jaw and strongly keeled dorsals. The third clade is characterized by a yellow iris, elongated lower jaw and weakly keeled dorsals. Despite their sympatric occurrence, every examined individual showed consistent grouping from mitochondrial, nuclear and morphological markers, indicating there is no gene flow among these three clades. Here, we describe the third clade as a new specie, Pareas atayal sp. nov.     

Molecular phylogeny of the marine littoral genus Cafius (Coleoptera: Staphylinidae: Staphylininae) and implications for classification

Jeon, M.‐J., Song, J.‐H. & Ahn, K.‐J. (2012). Molecular phylogeny of the marine littoral genus Cafius (Coleoptera: Staphylinidae: Staphylininae) and implications for classification. —Zoologica Scripta, 41, 150–159. A phylogenetic analysis of the marine littoral genus Cafius Stephens is presented based on molecular characters. The data set comprised partial mitochondrial COI (910 bp), COII (369 bp), 12S rDNA (351–354 bp), 16S rDNA (505–509 bp) and nearly complete sequences of 18S rDNA (1814–1830 bp) for 37 species. Twenty‐seven Cafius species, representing five of six subgenera, two Remus Holme species, three Phucobius Sharp species, monotypic Thinocafius Steel and four outgroups were included. The sequences were analysed simultaneously by parsimony analysis in Tree Analysis Using New Technology (TNT) with traditional manual alignment, direct optimization (DO) in the program POY4 under a variety of gap costs and partitioned Bayesian analysis for the combined data. The genus Cafius and nearly all of its subgenera were not supported as being monophyletic. Instead, all analyses (parsimony trees, DO tree under equal weighting and Bayesian tree) showed monophyly of Cafius + Phucobius + Remus + Thinocafius (clade Z) and all seven nested clades (A–G). However, the phylogenetic relationships among clades A–G differed among the analyses. The genus Phucobius was recovered as a monophyletic group within Cafius. The genus Remus was not monophyletic but formed a clade with C. rufescens Sharp and C. rufifrons Bierig within Cafius. The genus Thinocafius formed a clade with C. caviceps Broun, C. litoreus (Broun) and C. quadriimpressus (White) within Cafius. We propose new concepts for the genus Cafius and its related genera, and the seven nested clades.     

MOLECULAR PHYLOGENY AND TAXONOMY OF THE AEGAGROPILA CLADE (CLADOPHORALES,ULVOPHYCEAE), INCLUDING THE DESCRIPTION OF AEGAGROPILOPSIS GEN. NOV. AND PSEUDOCLADOPHORA GEN. NOV.1

The Aegagropila clade represents a unique group of cladophoralean green algae occurring mainly in brackish and freshwater environments. The clade is sister to the species‐rich and primarily marine Cladophora and Siphonocladus lineages. Phylogenetic analyses of partial LSU and SSU nrDNA sequences reveal four main lineages within the Aegagropila clade, and allow a taxonomic reassessment. One lineage consists of two marine ‘Cladophora’ species, for which the new genus Pseudocladophora and the new family Pseudocladophoraceae are proposed. For the other lineages, the family name Pithophoraceae is reinstated. Within the Pithophoraceae, the earliest diverging lineage includes Wittrockiella and Cladophorella calcicola, occurring mainly in brackish and subaerial habitats. The two other lineages are restricted to freshwater. One of them shows a strong tendency for epizoism, and consists of Basicladia species and Arnoldiella conchophila. The other lineage includes Aegagropila, Pithophora and a small number of tropical ‘Cladophora’ species. The latter are transferred to the new genus Aegagropilopsis. Previously, polypyramidal pyrenoids had been suggested to be apomorphous for this clade, but we report the finding of both polypyramidal and bilenticular pyrenoids in members of the Pithophoraceae, and thus show that this character has no diagnostic value.     

Molecular systematics and Holarctic phylogeography of cestodes of the genus Anoplocephaloides Baer, 1923 s. s. (Cyclophyllidea,Anoplocephalidae) in lemmings (Lemmus,Synaptomys)

The present molecular systematic and phylogeographic analysis is based on sequences of cytochrome c oxidase subunit 1 (cox1) (mtDNA) and 28S ribosomal DNA and includes 59 isolates of cestodes of the genus Anoplocephaloides Baer, 1923 s. s. (Cyclophyllidea, Anoplocephalidae) from arvicoline rodents (lemmings and voles) in the Holarctic region. The emphasis is on Anoplocephaloides lemmi (Rausch 1952) parasitizing Lemmus trimucronatus and Lemmus sibiricus in the northern parts of North America and Arctic coast of Siberia, and Anoplocephaloides kontrimavichusi (Rausch 1976) parasitizing Synaptomys borealis in Alaska and British Columbia. The cox1 data, 28S data and their concatenated data all suggest that A. lemmi and A. kontrimavichusi are both non‐monophyletic, each consisting of two separate, well‐defined clades, that is independent species. As an example, the sister group of the clade 1 of A. lemmi, evidently representing the ‘type clade’ of this species, is the clade 1 of A. kontrimavichusi. For A. kontrimavichusi, it is not known which one is the type clade. There is also fairly strong evidence for the non‐monophyly of Anoplocephaloides dentata (Galli‐Valerio, 1905)‐like species, although an earlier phylogeny suggested that this multispecies assemblage may be monophyletic. The results suggest a deep phylogenetic codivergence of Lemmus spp. and A. lemmi, primarily separating the two largely allopatric host and parasite species at the Kolyma River in east Siberia. There are also two allopatric sublineages within each main clade/species of A. lemmi and Lemmus, but the present distributions of the sublineages within the eastern L. trimucronatus and clade 1 of A. lemmi are not concordant. This discrepancy may be most parsimoniously explained by an extensive westward distributional shift of the easternmost parasite subclade. The results further suggest that the clade 1 of A. kontrimavichusi has diverged through a host shift from the precursor of L. trimucronatus to S. borealis.     

Length‐weight and length‐length relationships of thirteen fish species from the lower Jinsha River,southwest China

Length‐weight and length‐length relationships were investigated for 13 freshwater fish species from the lower Jinsha River, southwest China (from 101°32′49.63″E; 26°35′38.27″N to 104°37′48.14″E; 28°45′59.55″N). Fish were sampled from five sites during 2014 and 2016, using trap‐nets, gillnets (major mesh size: 2–6 cm), longline and electrofishing. Length‐weight relationships for six and length‐length relationships for 12 species are the first report to FishBase, respectively. Moreover, new maximum length for 11 species are also presented to FishBase in this study. All regressions were highly significant (p < .001), with the coefficient of determination r² > .950. These information will be helpful for management and conservation in local fishes and fisheries.     

Phylogeography and taxonomic status of trout and salmon from the Ponto‐Caspian drainages,with inferences on European Brown Trout evolution and taxonomy

Current taxonomy of western Eurasian trout leaves a number of questions open; it is not clear to what extent some species are distinct genetically and morphologically. The purpose of this paper was to explore phylogeography and species boundaries in freshwater and anadromous trout from the drainages of the Black and the Caspian Seas (Ponto‐Caspian). We studied morphology and mitochondrial phylogeny, combining samples from the western Caucasus within the potential range of five nominal species of trout that are thought to inhabit this region, and using the sequences available from GenBank. Our results suggest that the genetic diversity of trout in the Ponto‐Caspian region is best explained with the fragmentation of catchments. (1) All trout species from Ponto‐Caspian belong to the same mitochondrial clade, separated from the other trout since the Pleistocene; (2) the southeastern Black Sea area is the most likely place of diversification of this clade, which is closely related to the clades from Anatolia; (3) The species from the Black Sea and the Caspian Sea drainages are monophyletic; (4) except for the basal lineage of the Ponto‐Caspian clade, Salmo rizeensis, all the lineages produce anadromous forms; (5) genetic diversification within the Ponto‐Caspian clade is related to Pleistocene glacial waves; (6) the described morphological differences between the species are not fully diagnostic, and some earlier described differences depend on body size; the differences between freshwater and marine forms exceed those between the different lineages. We suggest a conservative taxonomic approach, using the names S. rizeensis and Salmo labrax for trout from the Black Sea basin and Salmo caspius and Salmo ciscaucasicus for the fish from the Caspian basin.     

Isolation and characterization of eight microsatellite loci for the Neotropical freshwater catfish Pimelodella chagresi (Teleostei: Pimelodidae)

We report eight (CA)_10?35 unlinked microsatellite loci from the Neotropical freshwater catfish, Pimelodella chagresi (Siluriformes: Pimelodidae). These loci were characterized with 23 individuals collected in Panama. Number of alleles per locus varied from 7 to 23 (mean = 12.9) and observed heterozygosity ranged from 0.522 to 0.909 (mean = 0.732). These loci will be used to investigate the existence of cryptic species within the P. chagresi clade, and to study fine‐scale population structure.     

Molecular phylogeny of African hinge‐back tortoises (Kinixys): implications for phylogeography and taxonomy (Testudines: Testudinidae)

We examine the phylogeography, phylogeny and taxonomy of hinge‐back tortoises using a comprehensive sampling of all currently recognized Kinixys species and subspecies and sequence data of three mitochondrial DNA fragments (2273 bp: 12S rRNA, ND4 + adjacent DNA coding for tRNAs, cytb) and three nuclear loci (2569 bp: C‐mos, ODC, R35). Combined and individual analyses of the two data sets using Bayesian and Maximum Likelihood methods suggest that the savannah species of Kinixys are paraphyletic with respect to the rainforest species K. homeana and K. erosa, and that the rainforest species may be derived from a savannah‐living ancestor. The previously recognized savannah species K. belliana was a conglomerate of three deeply divergent clades that we treat here as distinct species. We restrict the name K. belliana (Gray, 1830) to hinge‐back tortoises ranging from Angola to Burundi, while five‐clawed hinge‐back tortoises from the northernmost part of the formerly recognized range of K. belliana, together with four‐clawed tortoises from West Africa, are assigned to the species K. nogueyi (Lataste, 1886). These two species are allied to K. spekii, whereas Southeast African and Malagasy hinge‐back tortoises formerly lumped together with K. belliana represent the distinct species K. zombensis Hewitt, 1931, which is sister to K. lobatsiana. The latter two species together constitute the sister group of the rainforest species K. homeana and K. erosa. Mitochondrial data suggest that K. natalensis has a basal phylogenetic position in a clade embracing K. belliana sensu stricto, K. nogueyi and K. spekii, while nuclear data and the two data sets combined favour a sister group relationship of K. natalensis to all other hinge‐back tortoises. Phylogeographic structure is present in all wide‐ranging species and correlates in K. homeana and K. erosa with the Dahomey Gap and former rainforest refugia. The Malagasy population of K. zombensis is weakly differentiated from its South African conspecifics and further sampling is needed to determine whether there is support for the subspecific distinctness of Malagasy tortoises.