Secondary contact between two divergent lineages of charrs of the genus <Emphasis Type="Italic">Salvelinus</Emphasis> in the Northwest Pacific

The present-day contact zone between the Beringian and Arctic phylogenetic lineages of charrs of the genus Salvelinus in the Northwest Pacific is documented. A comparative analysis of the genetic differentiation and divergence indices for allopatric and sympatric populations of charrs and phylogenetic and genealogical analyses of the mtDNA haplotypes indicate that Lake Achchen and the Lake Pekulineiskoe are the zones of secondary contact between S. m. malma and S. taranetzi; Lake Nachikinskoe, between S. m. malma and Salvelinus sp. 4; and Lake Dal’nee, between S. m. malma and S. krogiusae. The level of divergence between phylogenetic groups of haplotypes considerably exceeds the range of intraspecific variability of S. m. malma and could not have been achieved after colonization of the lakes in conditions of sympathy. The obtained data suggest that the territory of Kamchatka was colonized by the common ancestor of the Arctic phylogroup of Taranetz charr.     

Taxonomic status and origin of some ecological forms of whitefish <Emphasis Type="Italic">Coregonus lavaretus</Emphasis> (L.) from water bodies of Siberia

Molecular genetic analysis of some ecological forms of whitefish belonging to the Coregonus lavaretus (L.) complex from different water bodies of Siberia revealed a high degree of differentiation between them. On the basis of the analysis of the mitochondrial DNA protein-coding ND1 gene, it was demonstrated that the previously described ecological forms of C. anaulorum, Yenisei River whitefish, or Issatschenko’s whitefish (C. fluviatilis), and cisco-like whitefish from Lake Baunt were good biological species. Moreover, each ecological form was represented by a number of phylogenetic lineages, one of which was species-specific. The remaining lineages were characterized by the mitochondrial DNA of another whitefish species, usually, the most common in each geographic region. The results of genetic analysis demonstrated that the formation of modern ecological forms of Siberian pidschian-like whitefish was accompanied by natural introgressive hybridization. It is suggested that most of the modern pidschian-like whitefish species originated as a result of reticulate evolution.     

Genetic polymorphism,haplotype distribution,and phylogeny of <Emphasis Type="Italic">Daphnia</Emphasis> (Cladocera: Anomopoda) species from the water bodies of russia as inferred from the 16S mtDNA gene sequencing

The data on the genetic polymorphism of the most widespread Daphnia species occupying different water bodies of Russia are presented. The phylogenetic relationships between the examined species were established, and the haplotype networks were constructed. A fragment of the 16S mitochondrial DNA gene was used as a genetic marker. The results of molecular phylogenetic analysis generally coincided with modern concepts in the systematics of the genus Daphnia. The representatives of the divergent mitochondrial lineages within the D. longispina, D. pulex, and D. magna complex remain poorly investigated morphologically. For D. dentifera, a new habitat on the territory of Russia, namely, the water bodies of the Lake Baikal basin, was identified. A conclusion was made that the 16S mtDNA gene could be successfully used in phylogeographic analysis of the genus Daphnia.     

A new primer set for amplification of the cytochrome <Emphasis Type="Italic">b</Emphasis> gene in lantern fishes (Myctophidae)

New universal primers are offered for amplification of complete sequence of mitochondrial cyt b gene in lantern fishes of the family Myctophidae. Analysis of cyt b variability in the species of seven genera (Bolinichthys, Ceratoscopelus, Diaphus, Diogenichthys, Lampanyctus, Lepidophanes, Nannobrachium) demonstrates considerable divergence between species: an average of 18.2% (p-distances). Diversity (nucleotide diversity, number of segregating and phylogenetically informative sites, average number of nucleotide differences) and divergence significantly exceed those of another widely used mitochondrial marker, a fragment of cytochrome c oxidase subunit 1 sequence (cox 1). The mitochondrial cyt b gene amplified with the developed primers can be recommended as an informative tool for phylogenetic and population studies of lantern fishes.     

Revision of the taxonomic status of the genus <Emphasis Type="Italic">Gloeoporus</Emphasis> (Polyporales,Basidiomycota) reveals two new species

Gloeoporus Mont. is characterized by an easily separated gelatinous hymenophore and a continuous hymenium over the pore mouth. Recent molecular taxonomic and phylogenetic research showed that morphological grouping of Gloeoporus is polyphyletic. The lack of comprehensive phylogenetic studies of Gloeoporus exacerbates confusion in determining the taxonomic position of the genus. To delimit the genus Gloeoporus, we performed multi-locus phylogenetic analysis using the internal transcribed spacer (ITS) region, the nuclear large subunit ribosomal DNA (LSU), and the second-largest subunit of RNA polymerase II (rpb2). The phylogenetic analyses revealed that current delimitation of Gloeoporus is not monophyletic. Gloeoporus s.s. includes mostly clamped species lacking cystidia. Some species of Gloeoporus featuring simple septa and cystidia are proposed to be renamed to Meruliopsis. Two new species of Gloeoporus were also observed and they are named Gloeoporus africanus and Gloeoporus orientalis.     

Efficiency of DNA barcoding for phylogenetic analysis and species identification in flying fish (Exocoetidae)

The article reports DNA barcoding (sequencing of the cox 1 mitochondrial gene fragment) of five South Atlantic flying fish species belonging to family Exocoetidae together with the results of the comparative analysis of cox 1 variability in the Exocoetidae and its closely related family Hemiramphidae. It has been demonstrated that DNA barcoding can be used as an extra tool for species identification and phylogenetic analysis in flying fish, since species identification accuracy using the cox 1 gene sequence proved to be 88%, or 78% when intraspecies variability level is taken into account. We have confirmed monophyletic origin of certain species, genera, and subfamilies of flying fish except for the genus Cheilopogon, which was represented on the phylogenetic tree by three paraphyletic clades. One of them shows close relationship to the genus Cypselurus, while another encompasses Hirundichthys genus species. The Exocoetidae is characterized by much lower overall genetic divergence level compared to the Hemiramphidae (average intraspecies differences: 10.2 ± 0.4% vs. 18.1 ± 0.8%; average intrageneric differences: 13.3 ± 1.1% vs. 21.3 ± 1.8%), which may indicate that the former group is relatively young in terms of evolution. No intraspecies differentiation was observed for Exocoetus obtusirostrus across a significant geographic distance (>3000 km). Phylogenetic reconstructions based on the variability of conservative (cox 1 mtDNA) and more variable regions of mitochondrial and nuclear genomes and on the adaptive morphological traits associated with gliding flight development were shown to coincide to a large extent.     

Microsatellite analysis supports the existence of three cryptic species within the bumble bee <Emphasis Type="Italic">Bombus lucorum sensu lato</Emphasis>

Mitochondrial cytochrome oxidase I (COI) partial sequences are widely used in taxonomy for species identification. Increasingly, these sequence identities are combined with modelling approaches to delineate species. Yet the validity of species delineation based on such DNA ‘barcodes’ is rarely tested and may be called into question by phenomena such as ancestral polymorphisms in DNA sequences, phylogeographic divergence, mitochondrial introgression and hybridization, or distortion of mitochondrial inheritance through such factors as Wolbachia infection. The common and widespread European bumble bee Bombus lucorum s. lato contains three distinct mitochondrial DNA lineages that are assumed to represent three cryptic species, namely Bombus cryptarum, B. lucorum s. str. and B. magnus. To test whether nuclear gene pools of the three putative species were differentiated, we genotyped 304 sympatric members of the lucorum complex (54 B. cryptarum females, 168 B. lucorum s. str. females and 82 B. magnus females, as defined using mtDNA COI haplotypes) from 11 localities spread across the island of Ireland at seven nuclear microsatellite loci. Multilocus genotypes clustered into three discrete groups that largely corresponded to the three mtDNA lineages: B. cryptarum, B. lucorum s. str. and B. magnus. The good fit of mitochondrial haplotype to nuclear (microsatellite) genotypic data supports the view that these three bumble bee taxa are reproductively isolated species, as well as providing a vindication of species identity using so-called DNA barcodes.     

Molecular phylogenetic analysis of key <Emphasis Type="Italic">Jatropha</Emphasis> species inferred from nrDNA ITS and chloroplast (<Emphasis Type="Italic">trn</Emphasis>L-F and <Emphasis Type="Italic">rbc</Emphasis>L) sequences

The genus Jatropha (Euphorbiaceae) contains species that are of significant economic and ornamental value. However, Jatropha breeding material is rather limited due to incomplete information regarding phylogenetic relationships among germplasm resources. Phylogenetic analyses were performed based on the internal transcribed spacer of nuclear ribosomal DNA (nrDNA ITS), two chloroplast regions (trnL-F and rbcL), and the combined (ITS+trnL-F+rbcL) dataset among twenty-five specimens representing six key Jatropha species. Phylogenetic relationships of Jatropha were well resolved between subgenus Curcas and subgenus Jatropha, and demonstrated the intermediate position of section Polymorphae among sections of both subgenera. Jatropha curcas and J. integerrima demonstrated a close phylogenetic relationship. The molecular data agreed with the morphological classification that recognized J. multifida and J. podagrica in sec. Peltatae. The distinct intraspecific divergence that occurred in J. curcas could be attributed to restricted gene flow caused by geographical isolation and different ecological conditions. Phylograms produced with trnL-F and rbcL sequence data suggested slow rates of sequence divergence among Jatropha spp., while the ITS gene tree had good resolution suggesting high genetic variation of ITS among Jatropha species.     

Phylogeny of the genus <Emphasis Type="Italic">Lophozia</Emphasis> (Dumort.) Dumort. s. str. inferred from nuclear and chloroplast sequences ITS1-2 and TRNL-F

Maximum parsimony and maximum likelihood phylogenetic trees were constructed for 21 taxa of Lophozia s. str. and the related genera, Schistochilopsis (5 species), Protolophozia elongata, and Obtusifolium obtusum based on combined nuclear ITS1-2 and chloroplast trnL-F DNA sequences. The trees were characterized by similar topology. It was demonstrated that the genus Lophozia s. str. was monophyletic, excluding L. sudetica, which deserved isolation into a distinct cryptic genus. The species distribution among the clades disagreed with the sections distinguished based on anatomical and morphological data. The relationships within the genus Schistochilopsis were consistent with the sectioning of the genus, based on morphological characters. Analysis of molecular data provided more precise definition of the systematic position of a number of taxa. A low level of genetic divergence of geographically distant forms was demonstrated.     

Genetic variation of Manchurian pheasant (<Emphasis Type="Italic">Phasianus colchicus pallasi</Emphasis> Rotshild, 1903) inferred from mitochondrial DNA control region sequences

Sequence variation of the mitochondrial DNA control region was studied in Manchurian pheasants (Phasianus colchicus pallasi Rotshild, 1903) representing three geographic populations from the southern part of the Russian Far East. Extremely low population genetic differentiation (F _ST = 0.0003) pointed to a very high gene exchange between the populations. Combination of such characters as high haplotype diversity (0.884 to 0.913), low nucleotide diversity (0.0016 to 0.0022), low R2 values (0.1235 to 0.1337), certain patterns of pairwise-difference distributions, and the absence of phylogenetic structure suggested that the phylogenetic history of Ph. c. pallasi included passing through a bottleneck with further expansion in the postglacial period. According to the data obtained, it was suggested that differentiation between the mitochondrial lineages started approximately 100000 years ago.     

Phylogeography of the Macaronesian Lettuce Species <Emphasis Type="Italic">Lactuca watsoniana</Emphasis> and <Emphasis Type="Italic">L. palmensis</Emphasis> (Asteraceae)

The phylogenetic relationships and phylogeography of two relatively rare Macaronesian Lactuca species, Lactuca watsoniana (Azores) and L. palmensis (Canary Islands), were, until this date, unclear. Karyological information of the Azorean species was also unknown. For this study, a chromosome count was performed and L. watsoniana showed 2n = 34. A phylogenetic approach was used to clarify the relationships of the Azorean endemic L. watsoniana and the La Palma endemic L. palmensis within the subtribe Lactucinae. Maximum parsimony, Maximum likelihood and Bayesian analysis of a combined molecular dataset (ITS and four chloroplast DNA regions) and molecular clock analyses were performed with the Macaronesian Lactuca species, as well as a TCS haplotype network. The analyses revealed that L. watsoniana and L. palmensis belong to different subclades of the Lactuca clade. Lactuca watsoniana showed a strongly supported phylogenetic relationship with North American species, while L. palmensis was closely related to L. tenerrima and L. inermis, from Europe and Africa. Lactuca watsoniana showed four single-island haplotypes. A divergence time estimation of the Macaronesian lineages was used to examine island colonization pathways. Results obtained with BEAST suggest a divergence of L. palmensis and L. watsoniana clades c. 11 million years ago, L. watsoniana diverged from its North American sister species c. 3.8 million years ago and L. palmensis diverged from its sister L. tenerrima, c. 1.3 million years ago, probably originating from an African ancestral lineage which colonized the Canary Islands. Divergence analyses with *BEAST indicate a more recent divergence of the L. watsoniana crown, c. 0.9 million years ago. In the Azores colonization, in a stepping stone, east-to-west dispersal pattern, associated with geological events might explain the current distribution range of L. watsoniana.     

<Emphasis Type="Italic">Phylloporia minutipora and P. radiata</Emphasis> spp. nov. (Hymenochaetales,Basidiomycota) from China and a key to worldwide species of <Emphasis Type="Italic">Phylloporia</Emphasis>

Phylloporia is a monophyletic genus within the Hymenochaetaceae as recovered by nuclear large subunit ribosomal DNA (nLSU) sequences. According to the summarization of 38 species accepted in this genus, Phylloporia is characterized by an absence of setae and the presence of abundant thick-walled, colored and tiny basidiospores, although its other morphological characters are highly diverse. Nine herbarium specimens from China, fitting the morphological concept of Phylloporia, were morphologically and phylogenetically studied in detail. The phylogeny inferred from nLSU sequences shows that the nine specimens formed three terminal lineages within the Phylloporia clade. Two lineages being composed of four specimens from Hainan and three from Guizhou were newly described as Phylloporia minutipora and P. radiata, respectively. In Phylloporia, P. minutipora is distinct by a combination of annual, sessile and imbricate basidiocarps, distinctly concentrically sulcate pileal surface with obtuse margin, angular pores of 12–15 per mm, duplex context separated by a black zone, a dimitic hyphal system, and broadly ellipsoid basidiospores of 2.5–3?×?2–2.5 μm, while P. radiata is distinct by a combination of annual, sessile and imbricate basidiocarps, faintly sulcate and radially striate pileal surface, sharp pileal margin, angular pores of 8–10 per mm, duplex context separated by a black zone, a monomitic hyphal system, and broadly ellipsoid basidiospores of 2.5–3.5?×?2–2.5 μm. The third lineage, comprising two specimens from Hainan, was morphologically determined as Phylloporia pulla. This species was recently combined to Phylloporia based on only morphological characters, and the current study for the first time generated its molecular sequences for phylogenetic reference. A key to all 40 species of Phylloporia is provided.     

Diversity and succession of pelagic microorganism communities in a newly restored Illinois River floodplain lake

Stenotopic specialization to a fragmented habitat promotes the evolution of genetic structure. It is not yet clear whether small-scale population structure generally translates into large-scale intraspecific divergence. In the present survey of mitochondrial genetic structure in the Lake Tanganyika endemic Altolamprologus (Teleostei, Cichlidae), a rock-dwelling cichlid genus comprising A. compressiceps and A. calvus, habitat-induced population fragmentation contrasts with weak phylogeographic structure and recent divergence among genetic clades. Low rates of dispersal, perhaps along gastropod shell beds that connect patches of rocky habitat, and periodic secondary contact during lake level fluctuations are apparently sufficient to maintain genetic connectivity within each of the two Altolamprologus species. The picture of genetic cohesion was interrupted by a single highly divergent haplotype clade in A. compressiceps restricted to the northern part of the lake. Comparisons between mitochondrial and nuclear phylogenetic reconstructions suggested that the divergent mitochondrial clade originated from ancient interspecific introgression. Finally, ‘isolation-with-migration’ models indicated that divergence between the two Altolamprologus species was recent (67–142 KYA) and proceeded with little if any gene flow. As in other rock-dwelling cichlids, recent population expansions were inferred in both Altolamprologus species, which may be connected with drastic lake level fluctuations.     

Complete mitochondrial genome of threatened mahseer <Emphasis Type="Italic">Tor tor</Emphasis> (Hamilton 1822) and its phylogenetic relationship within Cyprinidae family

The mahseers (Tor, Neolissochilus and Naziritor) are an important group of fishes endemic to Asia with the conservation status of most species evaluated as threatened. Conservation plans to revive these declining wild populations are hindered by unstable taxonomy. Molecular phylogeny studies with mitochondrial genome have been successfully used to reconstruct the phylogenetic tree and to resolve taxonomic ambiguity. In the present study, complete mitochondrial genome of Tor tor has been sequenced using ion torrent next-generation sequencing platform with coverage of more than 1000 ×. Comparative mitogenome analysis shows higher divergence value at ND1 gene than COI gene. Further, occurrence of a distinct genetic lineage of T. tor is revealed. The phylogenetic relationship among mahseer group has been defined as Neolissochilus hexagonolepis ((T. sinensis (T. putitora, T. tor), (T. khudree, T. tambroides)).     

Identification of Japanese <Emphasis Type="Italic">Lymantria</Emphasis> species (Lepidoptera: Lymantriidae) based on DNA sequences

We examined the utility of the cytochrome c oxidase subunit I (COI) and II (COII) genes of mitochondrial DNA (mtDNA) as a tool to identify nine Japanese Lymantria species, including four Asian gypsy moth species [Lymantria dispar japonica (Motschulsky), Lymantria umbrosa (Butler), Lymantria albescens Hori and Umeno, and Lymantria postalba Inoue]. In phylogenetic trees constructed for the COI and COII genes using the maximum likelihood methods, we could identify seven out of the nine Lymantria species (L. albescens and L. postalba could not be identified). These results suggest that the DNA sequences of the COI and COII genes are useful for identifying Japanese Lymantria species.     

A molecular phylogeny of the Old World cypresses (<Emphasis Type="Italic">Cupressus</Emphasis>: Cupressaceae): evidence from nuclear and chloroplast DNA sequences

Studies of phylogenetic relationships among cypresses of the Old World (Cupressus; Cupressaceae) have been plagued by unresolved relationships, poor branch support, and conflict between data sets and methods of analysis. In this study, we combined 5.4 kb of aligned DNA sequence and 157 binary characters with previously published data in examining phylogenetic relationships among Cupressus species. Bayesian and parsimony analysis of the combined data or of the nuclear data alone always recovered three principal clades of Cupressus; however, tests of phylogenetic incongruence could not distinguish between competing relationships among the three principal Cupressus lineages. In contrast, incongruence tests often found statistically significant conflict between the nuclear and plastid data, particularly with respect to the placement of C. chengiana. Consistent with previous studies and prevailing taxonomic opinion, we find C. darjeelingensis more closely related to cypresses of the New World (Hesperocyparis). In contrast, we placed accessions of C. assamica and C. tonkinensis, two putatively Old World species suggested to be misidentified New World taxa by some authors, within well-supported Old World clades. Statistical analysis of genetic distances suggests instances in which taxa recognized as distinct species by some authors are identical or nearly so and may best be considered a single taxon. Conversely, we identify instances in which infraspecific taxa are more distantly related to one another than those traditionally recognized as distinct species. Factors confounding cypress taxonomies, including poor morphological differentiation, misidentification, and the use of accessions of questionable provenance, are discussed.     

Tribal assignment of <Emphasis Type="Italic">Heldreichia</Emphasis> Boiss. (Brassicaceae): evidence from nuclear ITS and plastidic <Emphasis Type="Italic">ndh</Emphasis>F markers

Heldreichia Boiss. is a monospecific genus mainly distributed in Anatolia and the Lebanon. Although morphological variation and infrageneric phylogenetic relationships were recently studied in detail, Heldreichia remained as one of the few orphan genera that have not yet been assigned to any tribe. In the current study, we used sequence data from the nuclear ITS and chloroplast ndhF regions of Heldreichia and representatives of main Brassicaceae lineages and tribes to determine its tribal affiliation. Bayesian-based phylogenetic analyses clearly show with high support that Heldreichia is a member of the recently expanded tribe Biscutelleae. Furthermore, we characterize the tribe Biscutelleae morphologically and provide a determination key for all its genera.