Extensive cryptic diversity in the cosmopolitan sludge worm <Emphasis Type="Italic">Limnodrilus hoffmeisteri</Emphasis> (Clitellata,Naididae)

Limnodrilus hoffmeisteri Claparède, 1862 is a common freshwater worm, often regarded as an indicator of organic pollution. The taxonomic status of this species is controversial due to great variation in morphological features. Numerous morphological forms of L. hoffmeisteri are recorded in the literature, especially from Europe and North America. Today, DNA-based species delimitation assumes that species boundaries can be more objectively and effectively estimated using genetic data rather than with morphological data alone. To investigate if L. hoffmeisteri is a single species, 295 worms identified as either L. hoffmeisteri or other similar (congeneric) morphospecies, using currently accepted morphological criteria, were collected from 82 locations in the northern hemisphere. The number of primary species hypotheses (PSHs) was first explored with cytochrome oxidase subunit I (COI), the proposed DNA barcode for animal species, and with data for all specimens. Both automatic barcoding gap discovery (ABGD) and the Bayesian general mixed Yule coalescent (bGMYC) model revealed the existence of ≥25 distinct PSHs (COI lineages) in our dataset. Then, smaller samples of individuals representing major COI lineages were used for exploration of a nuclear locus, the internal transcribed spacer (ITS) region. In the ITS gene tree (81 sequences), generated by BEAST, 16 well-supported terminal groups were found, but not all of these groups were congruent with the PSHs found in the COI tree. As results across these different analyses were inconsistent, we resorted to analyzing reciprocal monophyly between gene trees and used a minimum consensus of all evidence, suggesting that there are 13 separately evolving lineages (=13 species) within our sample. The smallest uncorrected COI p-distance between these species is 12.1%, and the largest intraspecific p-distance is 16.4%, illustrating the problem of species delimitation with a DNA-barcoding gap as the sole criterion. Ten of these species are morphologically identified as “L. hoffmeisteri,” the remaining three can be attributed to morphologically distinct congeneric species. An individual from the type locality in Switzerland was designated as a neotype of L. hoffmeisteri sensu stricto. This worm belongs to one of the ten species, and this lineage is widely distributed in Europe, Asia, and North America. The remaining nine species show a mixed distribution pattern; some appear to be endemic to a restricted area, others are Holarctic. Our results provide clues to the future revalidation of some of the nominal species today placed in synonymy with L. hoffmeisteri. A BEAST analysis, based on previously published and newly generated 16S data, suggested that this complex contains also other species than those studied by us. By integrating additional genetic data, it will be possible to identify these and additional specimens in future studies of Limnodrilus, and the neotype provides a baseline for further revisions of the taxonomy of the L. hoffmeisteri complex.     

Historical range contraction,and not taxonomy,explains the contemporary genetic structure of the Australian tree <Emphasis Type="Italic">Acacia dealbata</Emphasis> Link

Irrespective of its causes, strong population genetic structure indicates a lack of gene flow. Understanding the processes that underlie such structure, and the spatial patterns it causes, is valuable for conservation efforts such as restoration. On the other hand, when a species is invasive outside its native range, such information can aid management in the non-native range. Here we explored the genetic characteristics of the Australian tree Acacia dealbata in its native range. Two subspecies of A. dealbata have previously been described based on morphology and environmental requirements, but recent phylogeographic data raised questions regarding the validity of this taxonomic subdivision. The species has been widely planted within and outside its native Australian range and is also a highly successful invasive species in many parts of the world. We employed microsatellite markers to investigate the population genetic diversity and structure among 42 A. dealbata populations from across the species’ native range. We also tested whether environmental variables purportedly relevant for the putative separation of subspecies are linked with population genetic differentiation. We found no relationship between population genetic structure of A. dealbata in Australia and these environmental features. Rather, we identified two geographically distinct genetic clusters that corresponded with populations in the northeastern part of mainland Australia, and the southern mainland and Tasmanian range of the species. Our results do not support the taxonomic subdivision of the species into two distinct subspecies based on environmental features. We therefore assume that the observed morphological differences between the putative subspecies are plastic phenotypic responses. This study provides population genetic information that will be useful for the conservation of the species within Australia as well as to better understand the invasion dynamics of A. dealbata.     

Taxonomic implications of the morphological and genetic variation of cultivated and domesticated populations of the <Emphasis Type="Italic">Agave angustifolia</Emphasis> complex (Agavoideae,Asparagaceae) in Oaxaca,Mexico

The Agave angustifolia complex, distributed from Mexico to Costa Rica, comprises four species and five varieties, including three species used for mescal production. The complex is represented in the Mexican state of Oaxaca by two wild taxa, A. angustifolia var. angustifolia and A. angustifolia var. rubescens, the cultivated form A. angustifolia “Espadín” and the partially cultivated species A. rodacantha. The aims of this study were to investigate the morphological and genetic variation of the A. angustifolia complex in the state of Oaxaca and to identify traits useful for taxonomic delimitation. Four wild and three cultivated populations of A. angustifolia from Oaxaca, one population of A. tequilana from Guanajuato and one population of A. angustifolia from Sonora were sampled for morphological, genetic and cytometric analyses. We showed that cultivated populations of A. angustifolia “Espadin,” A. rhodacantha and A. tequilana could be clearly differentiated from wild populations. Furthermore, the domesticated populations of A. angustifolia, known locally as “Espadin,” had a higher ploidy level and lower genetic variation than their related wild populations. The population of A. angustifolia from Sonora could be recognized as a different entity. Populations of A. rhodacantha need to be studied throughout their entire distribution area to further evaluate their taxonomic delimitation.     

The taxonomic challenge posed by the Antarctic echinoids <Emphasis Type="Italic">Abatus bidens</Emphasis> and <Emphasis Type="Italic">Abatus cavernosus</Emphasis> (Schizasteridae,Echinoidea)

Cryptic species have been repeatedly described for two decades among the Antarctic fauna, challenging the classic model of Antarctic species with circumpolar distributions and leading to revisit the richness of the Antarctic fauna. No cryptic species had been so far recorded among Antarctic echinoids, which are, however, relatively well diversified in the Southern Ocean. The R/V Polarstern cruise PS81 (ANT XXIX/3) came across populations of Abatus bidens, a schizasterid so far known by few specimens that were found living in sympatry with the species Abatus cavernosus. The species A. cavernosus is reported to have a circum-Antarctic distribution, while A. bidens is only recorded with certainty in South Georgia and at the northern tip of the Antarctic Peninsula. Based on genetic and morphological analyses, our results clearly show that A. bidens and A. cavernosus are two distinct species. The analyzed specimens of A. bidens group together in two haplogroups separated from one another by 2.7 % of nucleotide differences. They are located in the Weddell Sea and in the Bransfield Strait. Specimens of A. cavernosus form one single haplogroup separated from haplogroups of A. bidens by 5 and 3.5 % of nucleotide differences, respectively. The species was collected in the Drake Passage and in the Bransfield Strait. Morphological analyses differentiate A. bidens from A. cavernosus. In contrast, the two genetic groups of A. bidens cannot be differentiated from one another based on morphology alone, suggesting that they may represent a case of cryptic species, common in many Antarctic taxa, but not yet reported in Antarctic echinoids. This needs to be confirmed by complementary analyses of independent genetic markers.     

Genetic and morphological diversity in <Emphasis Type="Italic">Tragopogon graminifolius</Emphasis> DC. (Asteraceae) in Iran

Tragopogon graminifolius DC. is a medicinal plant species of the genus Tragopogon L. (Asteraceae) that grows in different regions of Iran and is extensively used by locals. There is no report on genetic variability and population structure of this important plant species. Therefore, we studied the genetic diversity, population structure and morphological variability of 14 geographical populations of Tragopogon graminifolius in Iran. AMOVA and Gst analyses revealed significant molecular differences among the studied populations. Mantel test showed significant correlation between genetic distance and geographical distance of the studied populations and indicated that the neighboring populations had a higher degree of gene flow. STRUCTURE plot identified three main gene pools for Tragopogon graminifolius in Iran and population assignment test revealed that gene flow occurred mostly among populations of the same gene flow. The studied populations differed significantly in their morphological and genetic features. These results may be of use for future conservation of this important plant species.     

Morphology and distribution of the North American diatom <Emphasis Type="Italic">Aulacoseira pardata</Emphasis> English &amp; Potapova in Russia

Diatom species Aulacoseira pardata English & Potapova, new for the flora of Russia, has been found in the course of studying samples from Lake Frolikha (Transbaikal region) by scanning electron microscopy. Numerical morphological features of the species in the studied population differ from the type population, which indicates their greater variability. It is shown that A. pardata is distinguished from the similar species A. septentrionalis (Camburn & Charles) Genkal & Kulikovskiy by the shape of spines and shape and size of areolae on the valve mantle. Species A. septentrionalis, new for the lake, as well as for Cis-Baikal and Transbaikal regions, has also been recorded in Lake Frolikha.     

<Emphasis Type="Italic">Cortinarius</Emphasis> sect. <Emphasis Type="Italic">Riederi</Emphasis>: taxonomy and phylogeny of the new section with European and North American distribution

Cortinarius is one of the most species-rich genera of mushroom-forming fungi. Based on phylogenetic and morphological evidence, Cortinarius, sect. Riederi, is introduced at sectional level (= subsect. Riederi sensu Brandrud & Melot). The taxonomy, phylogeny, ecology and distribution of not only mainly European but also including some North American taxa of this section are treated, which includes nine species and two varieties. Of these, three taxa are described as new (C. burlinghamiae, C. pallidoriederi and C. argenteolilacinus var. dovrensis). The sect. Riederi species possess morphological features similar to Phlegmacium group(s) and forms a phylogenetically isolated lineage, with no supported affinity to other phlegmacioid groups. Three taxa are known from both Europe and North America, two species are known only from North America and five only from Europe. Altogether, eight of the ten taxa are associated with conifers or northern (boreal-subalpine) deciduous trees (Betula spp.). Only two species occur in more temperate forests (Fagus forests), and no species have so far been found in thermophilous Quercus forests     

Population structure and variability of Pacific herring (<Emphasis Type="Italic">Clupea pallasii</Emphasis>) in the White Sea,Barents and Kara Seas revealed by microsatellite DNA analyses

Pacific herring, Clupea pallasii, have recently colonised the northeast Atlantic and Arctic Oceans in the early Holocene. In a relatively short evolutionary time, the herring formed a community with a complex population structure. Previous genetic studies based on morphological, allozyme and mitochondrial DNA data have supported the existence of two herring subspecies from the White Sea and eastern Barents and Kara Seas (C. p. marisalbi and C. p. suworowi, respectively). However, the population structure of the White Sea herring has long been debated and remains controversial. The analyses of morphological and allozyme data have previously identified local spawning groups of herring in the White Sea, whereas mtDNA markers have not revealed any differentiation. We conducted one of the first studies of microsatellite variation for the purpose of investigating the genetic structure and relationship of Pacific herring among ten localities in the White Sea, the Barents Sea and the Kara Sea. Using classical genetic variance-based methods (hierarchical AMOVA, overall and pairwise F _ST comparisons), as well as the Bayesian clustering, we infer considerable genetic diversity and population structure in herring at ten microsatellite loci. Genetic differentiation was the most pronounced between the White Sea (C. p. marisalbi) versus the Barents and Kara seas (Chesha–Pechora herring, C. p. suworowi). While microsatellite variation in all C. pallasii was considerable, genetic diversity was significantly lower in C. p. suworowi, than in C. p. marisalbi. Also, tests of genetic differentiation were indicating significant differentiation within the White Sea herring between sympatric summer- and spring-spawning groups, in comparison with genetic homogeneity of the Chesha–Pechora herring.     

A morphological and phylogenetic analysis of <Emphasis Type="Italic">Ornithodoros marinkellei</Emphasis> (Acari: Argasidae), with additional notes on habitat and host usage

Ornithodoros marinkellei was described from larvae collected on Pteronotus spp. bats in Colombia and Panama. More recently, this tick was reported in the Brazilian Amazon. Because some morphometric differences were observed between O. marinkellei larvae from Colombia and Brazil, it was proposed that further investigations were needed to assess whether the differences could be attributed to intra- or inter-specific polymorphism. Herein, we collected O. marinkellei specimens in the type locality of Colombia, in Brazil, and in a new locality in Nicaragua, expanding the distribution of the species to Nicaragua. Morphometric analysis of larvae and adults, corroborated by a principal component analysis (PCA), indicated that the Brazilian specimens were larger than specimens from Colombia and Nicaragua. Phylogenetic analysis inferred from the mitochondrial 16S rRNA gene showed ticks from Colombia and Nicaragua more genetically related than any of them with ticks from Brazil, although ticks from the three countries grouped in a clade sister to a major clade containing sequences of various Neotropical Ornithodoros species. We concluded that ticks identified as O. marinkellei from Colombia, Nicaragua, and Brazil represent the same taxon, and that the genetic and morphological differences between them are likely to have a geographical bias. We redescribed the nymph of O. marinkellei, which has a vestigial hypostome, probably incompatible with blood feeding. We also report human infestation by O. marinkellei adults. As all reports of O. marinkellei adults have been from hot caves (temperature?>?35 °C), this abiotic condition could be a limiting factor for the occurrence of this tick species.     

Modern State of Populations of Endemic <Emphasis Type="Italic">Oxytropis</Emphasis> Species from Baikal Siberia and Their Phylogenetic Relationships Based on Chloroplast DNA Markers

The genetic diversity and population structure of the endemic species of Baikal Siberia Oxytropis triphylla, O. bargusinensis, and O. interposita were studied for the first time on the basis of the nucleotide polymorphism of intergenic spacers psbA–trnH, trnL–trnF, and trnS–trnG of chloroplast DNA. All populations of these species were characterized by a high haplotype (0.762–0.924) and relatively low nucleotide (0.0011–0.0022) diversity. Analysis of the distribution of variability in O. triphylla and O. bargusinensis showed that there was no significant genetic differentiation between populations of each species; the gene flow was 4.43 and 8.91, respectively. The high level of genetic diversity in the studied populations indicates a relatively stable state of these populations. A study of the phylogenetic relationships of closely related species confirms the concept of the origin of O. bargusinensis and O. tompudae as a result of intersectional hybridization of the species of the sections Orobia and Verticillares.     

Molecular genetic diversification of the lizard complex <Emphasis Type="Italic">Darevskia raddei</Emphasis> (Sauria: Lacertidae): Early stages of speciation

To characterize the molecular genetic diversity of the genus Darevskia, several populations were examined by the inter-SINE-PCR method, reporting the number and sizes of the spacers between individual copies of SINE-like interspersed repeats. Examination of 17 D. raddei geographical populations and several reference species revealed unequal genetic differences, measured as Nei and Li’s genetic distances (D_NL), for different groups of samples. The highest homogeneity was observed for the apparently panmictic D. raddei nairensis population from the basin of the Hrazdan River: genetic differences within each of the five samples and between them were similarly low (less than 0.1). The difference between ten samples of D. raddei raddei from Armenia and Karabakh (0.2–0.3) was somewhat higher than the interindividual difference within each sample (0.1–0.2), indicating that the samples belonged to different populations. The assumption was supported by the phylogenetic tree topology and multidimensional scaling. The differences between samples from the morphological subspecies D. raddei raddei and D. raddei nairensis ranged 0.3–0.4. The difference of two D. raddei raddei samples of Talysh (Azerbaijan) from other samples of the same subspecies corresponded to the subspecific level. The genetic distances between the good species D. raddei and D. rudis was 0.6–0.7. In terms of D_NL, a questionable population from northwestern Turkey (“D. tristis”) was closer to D. rudis (D_NL = 0.45), probably representing its subspecies. The phylogeography of D. raddei is discussed.     

A re-evaluation of diversity of the Aporocotylidae Odhner, 1912 in <Emphasis Type="Italic">Siganus fuscescens</Emphasis> (Houttuyn) (Perciformes: Siganidae) and associated species

The aporocotylid fauna of the mottled spinefoot, Siganus fuscescens (Houttuyn), from Moreton Bay, Queensland, Australia, was characterised using a combined morphological and molecular approach. Four aporocotylid species were identified, three belonging to the genus Ankistromeces Nolan & Cribb, 2006 and one to Cardicola Short, 1953. Specimens of Cardicola matched an undescribed species from the same host and locality; this species is described as Cardicola mogilae n. sp. Phylogenetic analyses of ITS2 and 28S data showed that C. mogilae n. sp. forms a strongly supported clade with other Cardicola species from siganid fishes. We record Ankistromeces olsoni Nolan & Cribb, 2006 in Moreton Bay for the first time, redescribe A. dunwichensis Nolan & Cribb, 2006 on the basis of new specimens and sequence data and re-report Ankistromeces sp. X from Moreton Bay based on molecular data. We review the status of the ten putative species of aporocotylids reported from siganids. Small variation in ITS2 rDNA sequences, in association with different geographic localities, was previously used to separate Cardicola lafii Nolan & Cribb, 2006 from C. parilus Nolan & Cribb, 2006, C. bartolii Nolan & Cribb, 2006 from C. watsonensis Nolan & Cribb, 2006, C. tantabiddii Nolan & Cribb, 2006 from Cardicola sp. 2, Ankistromeces sp. Y from A. olsoni and Ankistromeces sp. X from Ankistromeces sp. Z. These five combinations are reinterpreted as each representing a single species; Cardicola lafii is recognised as the senior synonym of C. parilus and C. bartolii as the senior synonym of C. watsonensis. This study thus suggests that six, rather than ten, species should be recognised as infecting S. fuscescens. This richness remains greater than is known for any other fish species and siganids are, so far, unique among fishes in harbouring two strongly radiated lineages of aporocotylids.     

Molecular genetic diversity of <Emphasis Type="Italic">Gongylonema neoplasticum</Emphasis> (Fibiger &amp; Ditlevsen, 1914) (Spirurida: Gongylonematidae) from rodents in Southeast Asia

More than a dozen Gongylonema spp. (Spirurida: Spiruroidea: Gongylonematidae) have been described from a variety of rodent hosts worldwide. Gongylonema neoplasticum (Fibiger & Ditlevsen, 1914), which dwells in the gastric mucosa of rats such as Rattus norvegicus (Berkenhout) and Rattus rattus (Linnaeus), is currently regarded as a cosmopolitan nematode in accordance with global dispersion of its definitive hosts beyond Asia. To facilitate the reliable specific differentiation of local rodent Gongylonema spp. from the cosmopolitan congener, the genetic characterisation of G. neoplasticum from Asian Rattus spp. in the original endemic area should be considered since the morphological identification of Gongylonema spp. is often difficult due to variations of critical phenotypical characters, e.g. spicule lengths and numbers of caudal papillae. In the present study, morphologically identified G. neoplasticum from 114 rats of seven species from Southeast Asia were selected from archived survey materials from almost 4,500 rodents: Thailand (58 rats), Cambodia (52 rats), Laos (three rats) and Philippines (one rat). In addition, several specimens from four rats in Indonesia were used in the study. Nucleotide sequences of the ribosomal RNA gene (rDNA) (5,649 bp) and the cytochrome c oxidase subunit 1 gene (cox1) (818 bp) were characterised. The rDNA showed little nucleotide variation, including the internal transcribed spacer (ITS) regions. The cox1 showed 24 haplotypes, with up to 15 (1.83%) nucleotide substitutions regardless of parasite origin. Considering that Rattus spp. have been shown to originate from the southern region of Asia and G. neoplasticum is their endogenous parasite, it is reasonable to propose that the present study covers a wide spectrum of the genetic diversity of G. neoplasticum, useful for both the molecular genetic speculation of the species and the molecular genetic differentiation of other local rodent Gongylonema spp. from the cosmopolitan congener.     

<Emphasis Type="Italic">Galerina saxicola</Emphasis> (Fungi,Agaricales) is conspecific with <Emphasis Type="Italic">G. stordalii</Emphasis> and new data on ecology of the latter species

The holotype of Galerina saxicola Svr?ek, a never revised species described from the Czech Republic in 1994, was studied in detail. Due to its poor state and the impossibility to obtain DNA data, we fixed its taxonomic position by designating an epitype using recent material from the type locality. The species proved to be conspecific with Norwegian and Czech collections of Galerina stordalii A.H.Sm., both morphologically and molecularly. Full synonymy and diagnostic characters of G. stordalii are provided, its morphological and ecological variability is discussed, and information on type specimens is corrected. Our collections document that G. stordalii has a broader ecological amplitude than thought before, living not only on Sphagnum and peat in boreal and arctic-alpine habitats like bogs and snow beds, but also among mosses in boggy spruce forests, on decaying conifer trunks in old-growth forests and on moist sandstone rocks in a river canyon under the influence of climatic inversion.     

A new Galeopid (Anomodontia,Galeopidae) from the Permian of Eastern Europe

A new anomodont genus and species, Parasuminia ivakhnenkoi sp. nov. (Galeopidae), from the Sundyr-1 locality (Upper Severodvinian Substage, Upper Permian) is described. Based on morphological analysis of tooth wear, the type of work of the jaw apparatus similar to that of Suminia Ivachnenko, 1994 is revealed.     

Comparative characteristics of North Pacific and North Atlantic specimens of a rare bathypelagic fish <Emphasis Type="Italic">Thalassobathia pelagica</Emphasis> (Teleostei: Bythitidae) with discussion of its distribution

A detailed morphological comparison is made of the North Pacific specimen of Thalassobathia pelagica with fish from the North Atlantic (the type locality). The Pacific specimen is recognized as conspecific with Atlantic ones. Insignificant differences are considered as age or individual variation. The structure of the seismosensory system of T. pelagica and morphology of this species are described in more detail. The probable distribution of T. pelagica is discussed. A wide tropical area of this species is assumed and a possibility of its presence in all three oceans. The captures of T. pelagica in high latitudes may depend on its transportation with warm currents.     

Identification and monitoring of Korean medicines derived from <Emphasis Type="Italic">Cinnamomum</Emphasis> spp. by using ITS and DNA marker

In this study, we identified and evaluated the genetic relationships among Cinnamomum plants, which are used in traditional medicine. We also attempted to monitor the distribution of traditional medicines derived from Cinnamomum cassia by using DNA barcoding and a species-specific DNA marker. Plants of the genus Cinnamomum, and in particular C. cassia, are commonly used as medicinal herbs in the form of Cinnamomi Ramulus, Cinnamomi Cortex, and Cassiae Cortex Interior. However, it is difficult to distinguish among different Cinnamomum species based on morphological features, and so to overcome this limitation, nucleotide sequences of the internal transcribed spacer (ITS) region of Cinnamomum DNA were determined and compared. On the basis of the discrepancy in determined ITS sequences, a 408-bp product, amplified by the primer pair CC F1/CC R3, was developed as a C. cassia-specific DNA marker. Using the developed DNA marker in combination with the ITS 2 nucleotide sequence, we monitored imported and commercially supplied medicinal products derived from Cinnamomum plants in markets in Korean, China, and Japan. The results revealed that most of the specimens monitored were derived from C. cassia.