Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus

Utilization of multiple putatively neutral DNA markers for inferring evolutionary history of species population is considered to be the most robust approach. Molecular population genetic studies have been conducted in many species of Anopheles genus, but studies based on single nucleotide polymorphism (SNP) data are still very scarce. Anopheles minimus is one of the principal malaria vectors of Southeast (SE) Asia including the Northeastern (NE) India. Although population genetic studies with mitochondrial genetic variation data have been utilized to infer phylogeography of the SE Asian populations of this species, limited information on the population structure and demography of Indian An. minimus is available. We herewith have developed multilocus nuclear genetic approach with SNP markers located in X chromosome of An. minimus in eight Indian and two SE Asian population samples (121 individual mosquitoes in total) to infer population history and test several hypotheses on the phylogeography of this species. While the Thai population sample of An. minimus presented the highest nucleotide diversity, majority of the Indian samples were also fairly diverse. In general, An. minimus populations were moderately substructured in the distribution range covering SE Asia and NE India, largely falling under three distinct genetic clusters. Moreover, demographic expansion events could be detected in the majority of the presently studied populations of An. minimus. Additional DNA sequencing of the mitochondrial COII region in a subset of the samples (40 individual mosquitoes) corroborated the existing hypothesis of Indian An. minimus falling under the earlier reported mitochondrial lineage B.     

Toward an inordinate fondness for stars,beetles and Lobophora? Species diversity of the genus Lobophora (Dictyotales,Phaeophyceae) in New Caledonia

Until the recent use of molecular markers, species diversity of Lobophora, an ecologically important brown algal genus with a worldwide distribution in temperate and tropical seas, has been critically underestimated. Using a DNA‐based taxonomic approach, we re‐examined diversity of the genus from New Caledonia in the Southwest Pacific Ocean. First, species were delineated using general mixed Yule coalescent‐based and barcoding gap approaches applied to a mitochondrial cox3 data set. Results were subsequently confirmed using chloroplast psbA and rbcL data sets. Species delimitation analyses agreed well across markers and delimitation algorithms, with the barcoding gap approach being slightly more conservative. Analyses of the cox3 data set resulted in 31–39 molecular operational taxonomic units (MOTUs), four of which are previously described species (L. asiatica, L. crassa, L. nigrescens s.l., L. pachyventera). Of the remaining MOTUs for which we obtained a representative number of sequences and results are corroborated across analyses and genes, we described 10 species de novo: L. abaculusa, L. abscondita, L. densa, L. dimorpha, L. gibbera, L. hederacea, L. monticola, L. petila, L. rosacea, and L. undulata. Our study presents an excellent case of how a traditional morphology‐based taxonomy fails to provide accurate estimates of algal diversity. Furthermore, the level of Lobophora diversity unveiled from a single locality in the Pacific Ocean raises important questions with respect to the global diversity of the genus, the distributions and range sizes of the individual species, as well as the mechanisms facilitating coexistence.     

Taxonomy of the long‐tailed mouse Oligoryzomys destructor (Sigmodontinae: Oryzomyini) with the designation of neotypes for Hesperomys destructor Tschudi, 1844 and Hesperomys melanostoma Tschudi, 1844

The genus Oligoryzomys, distributed from southern South America to southern North America, is the most diverse of the tribe Oryzomyini of sigmodontine rodents. Even when 22 species are currently recognized, species boundaries are unclear for several forms. The species Oligoryzomys destructor is one of the least studied species of the genus and is the one with the largest distribution along the Andes (from southern Colombia to northern Bolivia). The species was described without the selection of a holotype and indication of its type locality. In addition, several taxa are regarded as synonyms of O. destructor. These facts are relevant because previous analysis of DNA sequences has shown that O. destructor represents a species complex. Herein, in addition to test the phylogenetic position of O. destructor within the genus Oligoryzomys, we assess patterns of morphological and molecular variation of O. destructor and its associated nominal forms aimed to assess the boundaries of the species. As part of the study, we selected neotypes for Hesperomys destructor and H. melanostoma. At the light of our results, we recognized O. destructor as a species with two subspecies, O. d. destructor and O. d. spodiurus. Also, we discuss the role of Andean rivers, and their different permeability, as allopatric barriers molding the structure of O. destructor.     

Sequencing type material resolves the identity and distribution of the generitype Lithophyllum incrustans,and related European species L. hibernicum and L. bathyporum (Corallinales,Rhodophyta)

DNA sequences from type material in the nongeniculate coralline genus Lithophyllum were used to unambiguously link some European species names to field‐collected specimens, thus providing a great advance over morpho‐anatomical identifi‐cation. In particular, sequence comparisons of rbcL, COI and psbA genes from field‐collected specimens allowed the following conclusion: the generitype species, L. incrustans, occurs mostly as subtidal rhodoliths and crusts on both Atlantic and Mediterranean coasts, and not as the common, NE Atlantic, epilithic, intertidal crust reported in the literature. The heterotypic type material of L. hibernicum was narrowed to one rhodolith belonging in Lithophyllum. As well as occurring as a subtidal rhodolith, L. hibernicum is a common, epilithic and epizoic crust in the intertidal zone from Ireland south to Mediterranean France. A set of four features distinguished L. incrustans from L. hibernicum, including epithallial cell diameter, pore canal shape of sporangial conceptacles and sporangium height and diameter. An rbcL sequence of the lectotype of Lithophyllum bathyporum, which was recently proposed to accommodate Atlantic intertidal collections of L. incrustans, corresponded to a distinct taxon hitherto known only from Brittany as the subtidal, bisporangial, lectotype, but also occurs intertidally in Atlantic Spain. Specimens from Ireland and France morpho‐anatomically identified as L. fasciculatum and a specimen from Cornwall likewise identified as L. duckerae were resolved as L. incrustans and L. hibernicum, respectively.     

Finding arboreal snakes in an evolutionary tree: phylogenetic placement and systematic revision of the Neotropical birdsnakes

The genus Pseustes Fitzinger, 1843 is composed of three recognized species, Pseustes poecilonotus, P. shropshirei and P. sulphureus, which may be the largest sized colubrid snake in the New World. The group has a complex systematic history that has yet to be untangled using modern molecular phylogenetic approaches. The systematic position, within‐group diversity and distribution are therefore uncertain. We obtained samples of four species from multiple specimens across their distribution and analysed one nuclear and two mitochondrial genes to determine the phylogenetic placement of the genus and infer relationships among Pseustes lineages. We find strong support for the paraphyly of Pseustes with respect to the monotypic genus Spilotes, both of which are nested within a clade of at least 23 other New World Colubrinae genera. Based on our results, we formally revise the taxonomy of P. poecilonotus and P. sulphureus, resurrecting the taxon P. polylepis for populations of P. poecilonotus from South America and allocating P. sulphureus to the genus Spilotes which renders both genera monophyletic. Additionally, we identify two lineages that are putatively new and currently unrecognized species. Finally, the placement of P. sulphureus, the type species of Pseustes, in the genus Spilotes, requires the allocation of the senior synonym Phrynonax be considered for the remaining Pseustes taxa.     

A phylogeographic investigation of the kelp genus Laminaria (Laminariales,Phaeophyceae), with emphasis on the South Atlantic Ocean

The genus Laminaria has a wide distribution range compared with other kelp genera because it is found in both the North and the South Atlantic, on both sides of the North Pacific, as well as in the Mediterranean. Hypotheses behind this biogeographical pattern have been discussed by several authors but have not yet been fully evaluated with time‐calibrated phylogenies. Based on the analysis of four molecular markers (ITS2, rbcL, atp8 and trnWI), our goal was to reassess the Laminaria species diversity in South Africa, assess its relationship with the other species distributed in the South Atlantic and reconstruct the historical biogeography of the genus. Our results confirm the occurrence of a single species, L. pallida, in southern Africa, and its sister relationship with the North Atlantic L. ochroleuca. Both species belonged to a clade containing the other South Atlantic species: L. abyssalis from Brazil, and the Mediterranean L. rodriguezii. Our time‐calibrated phylogenies suggest that Laminaria originated in the northern Pacific around 25 mya, followed by at least two migration events through the Bering Strait after its opening (~5.32 mya). Today, the first is represented by L. solidungula in the Arctic, while the second gave rise to the rest of the Atlantic species. The colonization of the North Atlantic was followed by a gradual colonization southward along the west coast of Europe, into the Mediterranean (~2.07 mya) and two recent, but disconnected, migrations (~1.34 and 0.87 mya) across the equator, giving rise to L. abyssalis in Brazil and L. pallida in southern Africa, respectively.     

Collections from the mesophytic zone off Bermuda reveal three species of Kallymeniaceae (Gigartinales,Rhodophyta) in genera with transoceanic distributions

A molecular survey of red algae collected by technical divers and submersibles from 90 m in the mesophotic zone off the coast of Bermuda revealed three species assignable to the Kallymeniaceae. Two of the species are representative of recently described genera centered in the western Pacific in Australia and New Zealand, Austrokallymenia and Psaromenia and the third from the Mediterranean Sea and the eastern Atlantic, Nothokallymenia. A phylogenetic analysis of concatenated mitochondrial (COI‐5P) and chloroplast (rbcL) genes, as well as morphological characteristics, revealed that two are shown to be new species with distant closest relatives (N. erosa and Psaromenia septentrionalis), while the third represents a deep water western Atlantic species now moved to an Australasian genus (A. westii).     

New insights into the molecular phylogeny and taxonomy of mormyrids (Osteoglossiformes,Actinopterygii) in northern East Africa

Based on morphological data and analysis of mitochondrial cytochrome b gene and nuclear (S7 intron 1) DNA sequences, the phylogenetic relationships of all Pollimyrus species known from the Omo‐Turkana enclosed basin and Nile system below the Murchison Falls were solved. A mormyrid “Pollimyrus” petherici is distantly related to all other studied Pollimyrus species and clusters together with Cyphomyrus species forming with the later a monophyletic group. Moreover, the West African (but not the Congo River) populations of Cyphomyrus psittacus, the type species of the genus, seem to be conspecific to C. petherici. That is, the range of the genus Cyphomyrus is extended toward the Nile and Omo‐Turkana basins. This genus belongs to the large clade widely distributed in sub‐Saharian Africa and characterized by the presence of a chin appendage. Significance of this character for mormyrid phylogeny is discussed. Two distinct lineages of Pollimyrus occurring sympatrically in the White Nile tributaries and previously reported as the light and dark forms of Pollimyrus isidori together with five other congeneric species studied form a monophyletic group. The light form apparently represents P. isidori distributed in the Nile system downstream of the Murchison Falls and West Africa; the dark‐colored form (designated as Pollimyrus “D”) represents a distinct phylogenetic lineage inhabiting both the Omo‐Turkana and the White Nile basin. Morphological and ecological data suggest that this form may be conspecific to East African Pollimyrus nigricans or most probably represents a new species.     

Transfer of the Thecate Amoeba Lecythium mutabilis to a Novel Genus Omnivora (Fiscullidae,Thecofilosea, Cercozoa)

Thecofilosea is a class in Cercozoa (Rhizaria) comprising mainly freshwater‐inhabiting algivores. Recently, numerous isolates of thecofilosean amoebae have been cultured and were characterized by an integrated morphological and molecular approach. As attempts to establish a culture of Lecythium mutabilis repeatedly failed, it was not yet investigated by molecular means. We isolated single cells of L. mutabilis directly from their habitat and successfully sequenced the V4 region of their SSU rDNA. Phylogenetic analyses showed that L. mutabilis is not directly related to the genus Lecythium and instead branches within the Fiscullidae (Tectofilosida, Thecofilosea). Accordingly, we transfer the species L. mutabilis to a novel genus Omnivora gen. nov.     

A Molecular Phylogenetic Study of the Tribe Corallineae (Corallinales,Rhodophyta) with an Assessment of Genus‐Level Taxonomic Features and Descriptions of Novel Genera

A multigene phylogeny using COI‐5P (mitochondrial cytochrome c oxidase subunit 1), psbA (PSII reaction center protein D1), and EF2 (elongation factor 2) sequence data for members of the tribe Corallineae was constructed to assess generic boundaries. We determined that traditional reliance on conceptacle position as an indicator of generic affinities in the Corallineae is not supported and taxonomic changes are required. We found that species currently assigned to Pseudolithophyllum muricatum resolved within the Corallineae in all analyses. This is the first record of crustose members in the subfamily Corallinoideae. Further‐more, the genus Serraticardia was polyphyletic; we propose to synonomize Serraticardia with Corallina, transfer the type species S. maxima to Corallina (C. maxima (Yendo) comb. nov.), and describe the new genus Johansenia for S. macmillanii (J. macmillanii (Yendo) comb. nov.). Our molecular data also indicate that species in the genus Marginisporum have evolutionary affinities among species of Corallina and these genera should also be synonymized. This necessitates the combinations C. aberrans (Yendo) comb. nov. for M. aberrans (Yendo) Johansen & Chihara, C. crassissima (Yendo) comb. nov. for M. crassissimum (Yendo) Ganesan, and C. declinata (Yendo) comb. nov. for M. declinata (Yendo) Ganesan. Corallina elongata was divergent from all other members of Corallina and is transferred to a new genus, Ellisolandia (E. elongata (J. Ellis & Solander) comb. nov). In addition, COI‐5P and internal transcribed spacer (ITS) data combined with morphological characters were used to establish that rather than the four Corallina species recognized in Canada, there are nine.     

Phylogenetic relationships,song and distribution of the endangered Rufous‐headed Robin Larvivora ruficeps

The Rufous‐headed Robin Larvivora ruficeps is one of the world's rarest and least known birds. We summarize the known records since it was first described in 1905 from Shaanxi Province, central China. All subsequent Chinese records are from seven adjacent localities in nearby Sichuan Province. We studied its phylogenetic position for the first time using mitochondrial and nuclear markers for all species of Larvivora and a broad selection of other species in the family Muscicapidae. Our results confirmed that L. ruficeps is appropriately placed in the genus Larvivora, and suggested that it is sister to the Rufous‐tailed Robin Larvivora sibilans, with these two forming a sister clade to a clade comprising both the Japanese Robin Larvivora akahige and Ryukyu Robin Larvivora komadori. Siberian Blue Robin Larvivora cyane and Indian Blue Robin Larvivora brunnea form the sister clade to the other Larvivora species. In contrast, song analyses indicated that the song of L. ruficeps is most similar to that of L. komadori, whereas the song of L. sibilans is relatively more similar to that of L. akahige, and songs of L. cyane and L. brunnea closely resemble each other. We used ecological niche modelling to estimate the suitable habitats of L. ruficeps based on the records from breeding grounds, suggesting that north and central Sichuan, south Gansu, south Shaanxi and south‐east Tibet are likely to contain the most suitable habitats for this species.     

Cyst‐motile stage relationship,morphology, ultrastructure,and molecular phylogeny of the gymnodinioid dinoflagellate Barrufeta resplendens comb. nov., formerly known as Gyrodinium resplendens,isolated from the Gulf of Mexico

In the present study, we redescribed Gyrodinium resplendens through incubation of process bearing cysts extracted from sediment collected in the northern Gulf of Mexico. The morphology and ultrastructure of the motile stage and cyst stage were examined using light microscopy, scanning electron microscopy, and transmission electron microscopy and this revealed that the species should be transferred to the genus Barrufeta. This genus differs from other gymnodinioid genera in possessing a Smurf‐cap apical structure complex (ASC) and currently encompasses only one species, Barrufeta bravensis. B. resplendens shows a Smurf‐cap ASC that consists of three rows of elongated vesicles with small knobs in the middle one. B. resplendens is very similar to B. bravensis in cell morphology, but can be separated using the ultrastructure such as the shape and location of nucleus and pyrenoids, which highlights the importance of ultrastructure at inter‐specific level in the genus Barrufeta. The unique cysts of B. resplendens are brown and process bearing, and have a tremic archeopyle with a zigzag margin on the dorsal side of the epicyst, and not polar as in cysts of Polykrikos. The cysts do not survive the palynological treatment used here and probably have a wide distribution. Maximum‐likelihood and Bayesian inference were carried out based on partial large subunit ribosomal DNA (LSU rDNA) sequences. Molecular phylogeny supports that the genus Barrufeta is monophyletic, and that the genus Gymnodinium is polyphyletic. Our results suggest that details of the ASC together with ultrastructure are potential features to subdivide the genus Gymnodinium.