scholarly journals First report of the order Mysida (Crustacea) in Antarctic marine ice caves, with description of a new species of Pseudomma and investigations on the taxonomy, morphology and life habits of Mysidetes species

ZooKeys ◽  
2021 ◽  
Vol 1079 ◽  
pp. 145-227
Author(s):  
Karl J. Wittmann ◽  
Pierre Chevaldonné
Keyword(s):  
Phylogenetic Trees ◽  
Developmental Stages ◽  
Sequence Data ◽  
Stomach Contents ◽  
Main Body ◽  
Feeding Apparatus ◽  
Trophic Conditions ◽  
Size Frequency Distribution ◽  
Rdna Sequences ◽  
Fat Bodies

SCUBA diving explorations of three islands off Dumont d’Urville Station at the coast of Adélie Land, East Antarctica, enabled the observation of marine ice caves. Sampling in this unusual habitat yielded a total of three species of Mysidae, altogether previously poorly known or unknown to science. Pseudomma kryotroglodytumsp. nov. is described, based on the structure of the antennal scale, telson and on cornea-like lateral portions set off against the main body of eyeplates. Mysidetes illigi is re-established at species level after almost a century in synonymy. Re-descriptions are provided for M. illigi and M. hanseni, based on types and ice cave materials. Keys to the Southern Ocean species of Pseudomma and to the world-wide species of Mysidetes are given. Phylogenetic trees are provided for the genera Pseudomma and Mysidetes. 18S rDNA sequences of P. kryotroglodytum differ from GenBank sequences of other Pseudomma species. First sequence data are given for species of the genus Mysidetes: 18S differs between the two examined species and COI is quite diverse between and within species. We found previously unknown, probably sensorial structures in these ice cave species: in P. kryotroglodytum, the basal segment of the antennula shows a pit-like depression with striated pad on the bottom and a median cyst, connected with the bottom of the eyeplate cleft. M. illigi shows a female homologue of the appendix masculina bearing a field of modified setae. Subsequent investigations demonstrated these structures also in species from other habitats. The feeding apparatus and stomach contents of the three ice cave species point to brushing of small particles (detritus, microalgae) from available surfaces, such as sediment, rock and the ice surface. Differences in the feeding apparatus are very subtle between the two Mysidetes species. The high content of fat bodies in M. hanseni could help it to survive periods of starvation. The large storage volume of the foregut in P. kryotroglodytum points to the collection of food with low nutritional quality and could help to balance strongly fluctuating food availability. Summer specimens of M. hanseni showed a bimodal frequency of developmental stages in the marsupium and bimodal size-frequency distribution of free-living stages. The females with younger brood (embryos) were, on average, larger and carried more marsupial young than those with older brood (nauplioid larvae). All examined incubating and spent females showed (almost) empty foreguts and empty ovarian tubes, suggesting possible semelparity and death following the release of young. The absence of juveniles and immature females from summer samples suggests that growth and accumulation of fat and yolk occur outside ice caves, while such caves could be used by fattened adults as shelter for brooding. A provisional interpretation proposes a biannual life cycle for M. hanseni, superimposed with shifted breeding schedules, the latter characterised by early breeding and late breeding females, probably in response to harsh physical and trophic conditions along the continental coast of Antarctica.

Molecular characterisation of some species of Mylonchulus (Nematoda: Mononchida) from Japan and comments on the status of Paramylonchulus and Pakmylonchulus

Nematology ◽  
2009 ◽  
Vol 11 (3) ◽  
pp. 337-342 ◽  
Author(s):  
Masaaki Araki ◽  
Wasim Ahmad ◽  
Majid Olia ◽  
Nobuhiro Minaka
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Data ◽  
Preliminary Investigation ◽  
Sister Group ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequences ◽  
The Status ◽  
Molecular Relationships ◽  
The Relationship

AbstractComparative analyses of different regions of ribosomal DNA have become a popular tool in understanding the relationship among different species and genera and nematodes are no exception to this. In this study, molecular relationships were inferred from a nearly complete small subunit (SSU) of total 16 OTUs for five species of Mylonchulus, Paramylonchulus and Pakmylonchulus collected from various parts of Japan with two out-group taxa (Mononchus aquaticus and Clarkus papillatus) to examine the relationship among these species. Out of 1685 bp SSU rDNA sequences, phylogenetic trees using distance (NJ), parsimony and likelihood algorithms were performed. Obtained tree topologies were stable across algorithms and sequence data show that populations of the same species clustered together and four out of five species (M. brachyuris, M. hawaiiensis, M. oceanicus, M. sigmaturus) formed a monophyletic assemblage while M. mulveyi formed a sister group. Populations of species lacking subventral teeth but with a double gonad (M. oceanicus) stand with other Mylonchulus species, thereby confirming the synonymy of Pakmylonchulus, while populations with a narrow buccal cavity with few rows of denticles, no subventral teeth and a single prodelphic gonad (M. mulveyi = Paramylonchulus mulveyi) support to some extent the validity of the genus Paramylonchulus. Though a preliminary investigation, it is the first report on molecular relationships in Mylonchulus, probably a paraphyletic genus. Our results suggest that SSU rDNA sequence data are useful in understanding the relationship between genera and species.

Clarification of the systematic position ofCercariaeum crassumWesenberg-Lund, 1934 (Digenea), based on karyological analysis and DNA sequences

2011 ◽  
Vol 86 (3) ◽  
pp. 293-301 ◽  
Author(s):  
R. Petkevičiūtė ◽  
V. Stunžėnas ◽  
G. Stanevičiūtė
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Developmental Stages ◽  
Sequence Divergence ◽  
Sister Group ◽  
Systematic Position ◽  
Life Cycles ◽  
Significant Information ◽  
Rdna Sequences ◽  
Species Specific

AbstractChromosome set and rDNA sequences of the larval digeneanCercariaeum crassumwere analysed in order to clarify its systematic position and possible adult form. Parasites were obtained from the sphaeriid bivalvePisidium amnicum, collected in Lithuanian and Finnish rivers. The karyotype is shown to consist of five pairs (2n = 10) of large, up to 14 μm, chromosomes. Complement, composed of a low diploid number of exclusively bi-armed elements, presumably arose through Robertsonian fusions of acrocentric chromosomes. Consistent with a Robertsonian-derived karyotype, one or two small, metacentric, mitotically stable B chromosomes were detected in the cells of parthenitae isolated from some host individuals. A phylogenetic analysis using rDNA internal transcribed spacer 2 (ITS2) and 28S sequences corroborates the allocation ofC. crassumto the family Allocreadiidae. In neighbour-joining and maximum parsimony phylogenetic treesC. crassumclusters into one clade withAllocreadiumspp., and is the closest sister group in relation toA. isoporum; the level of rDNA sequence divergence between them (2.67% for ITS2 and 1.16% for 28S) is consistent with the level expected for intrageneric variation. The present study adds significant information to a database for establishing species-specific characters for confident characterization of different developmental stages of allocreadiid species, clarification of their life cycles and evaluation of intra- and interspecific variability.

Exploring species diversity of lissorchiid trematodes (Digenea: Lissorchiidae) associated with the gravel snail, Lithoglyphus naticoides, in European freshwaters

2020 ◽  
Vol 94 ◽  
Author(s):  
R. Petkevičiūtė ◽  
G. Stanevičiūtė ◽  
V. Stunžėnas
Keyword(s):  
Developmental Stages ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Rutilus Rutilus ◽  
Life Cycles ◽  
Species Identity ◽  
Generic Level ◽  
Rdna Sequences ◽  
28S Rdna Sequence ◽  
Lithoglyphus Naticoides

Abstract Comparative analysis using complete ITS2 and partial 28S rDNA sequence data revealed that cercariaeum developing in rediae in Lithoglyphus naticoides represent two different lissorchiid species. One morphotype of cercariaeum is conspecific with adult Palaeorchis incognitus from European roach, Rutilus rutilus. The other cercariaeum is attributable to the genus Asymphylodora, but the species identity is not yet determined. We also generate the first rDNA sequences for Asymphylodora progenetica based on new collections from Bithynia tentaculata from Lithuania. Phylogenetic analyses of the newly generated sequences, together with information for other lissorchiids available on GenBank, showed that all representatives of Lissorchiidae form a strongly supported clade. Three monophyletic lineages, Asymphylodora, Palaeorchis and Lissorchis, were recognized at the generic level. Karyological analysis of the chromosome set of larval P. incognitus revealed a diploid number of 2n = 20. Its karyotype with subtelocentric chromosomes prevailing can be regarded as comparatively ‘primitive’, which is consistent with the basal position of P. incognitus in the 28S tree relative to the representatives of the genus Asymphylodora. The present study adds significant new information for establishing species-specific markers for the confident characterization of different developmental stages of lissorchiid species and clarification of their life cycles.

Effects of Predation and Trophic Conditions on the Reproduction of Tylototriton verrucosus (Caudata: Salamandridae) in Darjeeling

2011 ◽  
Vol 4 (2) ◽  
pp. 163-169 ◽  
Author(s):  
Ritwik Dasgupta
Keyword(s):  
Frequency Distribution ◽  
Primary Productivity ◽  
Egg Size ◽  
Zooplankton Abundance ◽  
Trophic Conditions ◽  
Size Frequency Distribution ◽  
Size Frequency ◽  
High Predation ◽  
Hatchling Size ◽  
Predation Rates

The facts that small hatchlings emerged from small eggs laid under high predation levels prevailing at the lower altitudes of distribution of this species in Darjeeling while larger hatchlings emerged from larger eggs laid under lower levels of predation at higher altitudes, show that predation is not selected for large egg and initial hatchling size in this salamandrid species. Metamorphic size was small under high predation rates because this species relied on crypsis for evading predators. Egg and hatchling size are related inversely to levels of primary productivity and zooplankton abundance in lentic habitats. Hatchling sizes are related positively to egg size and size frequency distribution of zooplankton. Small egg and small hatchling size have been selected for at the lower altitudes of distribution of this salamandrid in Darjeeling because predation rates increased in step with improvement in trophic conditions at the lower altitudes.

Population genetics, phylogeography, and systematics of the thornyhead rockfishes (Sebastolobus) along the deep continental slopes of the North Pacific Ocean

2000 ◽  
Vol 57 (8) ◽  
pp. 1701-1717 ◽  
Author(s):  
Carol A Stepien ◽  
Alison K Dillon ◽  
Amy K Patterson
Keyword(s):  
Pacific Ocean ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
North Pacific Ocean ◽  
Geographic Distance ◽  
The North ◽  
Continental Slopes ◽  
Genetic Patterns ◽  
Northern Pacific ◽  
Shortspine Thornyhead

Population genetic, phylogeographic, and systematic relationships are elucidated among the three species comprising the thornyhead rockfish genus Sebastolobus (Teleostei: Scorpaenidae). Genetic variation among sampling sites representing their extensive ranges along the deep continental slopes of the northern Pacific Ocean is compared using sequence data from the left domain of the mtDNA control region. Comparisons are made among the shortspine thornyhead (S. alascanus) (from seven locations), the longspine thornyhead (S. altivelis) (from five sites), which are sympatric in the northeast, and the broadbanded thornyhead (S. macrochir) (a single site) from the northwest. Phylogenetic trees rooted to Sebastes show that S. macrochir is the sister taxon of S. alascanus and S. altivelis. Intraspecific genetic variability is appreciable, with most individuals having unique haplotypes. Gene flow is substantial among some locations and others diverged significantly. Genetic divergences among sampling sites for S. alascanus indicate an isolation by geographic distance pattern. Genetic divergences for S. altivelis are unrelated to the hypothesis of isolation by geographic distance and appear to be more consistent with the hypothesis of larval retention in currents and gyres. Differences in geographic genetic patterns between the species are attributed to life history differences in their relative mobilities as juveniles and adults.

scholarly journals Origin of the European avian-like swine influenza viruses

2014 ◽  
Vol 95 (11) ◽  
pp. 2372-2376 ◽  
Author(s):  
Andi Krumbholz ◽  
Jeannette Lange ◽  
Andreas Sauerbrei ◽  
Marco Groth ◽  
Matthias Platzer ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Swine Influenza ◽  
H1n1 Influenza ◽  
Molecular Data ◽  
Influenza Viruses ◽  
Time Resolved ◽  
Genotype Constellation ◽  
Tree Inference

The avian-like swine influenza viruses emerged in 1979 in Belgium and Germany. Thereafter, they spread through many European swine-producing countries, replaced the circulating classical swine H1N1 influenza viruses, and became endemic. Serological and subsequent molecular data indicated an avian source, but details remained obscure due to a lack of relevant avian influenza virus sequence data. Here, the origin of the European avian-like swine influenza viruses was analysed using a collection of 16 European swine H1N1 influenza viruses sampled in 1979–1981 in Germany, the Netherlands, Belgium, Italy and France, as well as several contemporaneous avian influenza viruses of various serotypes. The phylogenetic trees suggested a triple reassortant with a unique genotype constellation. Time-resolved maximum clade credibility trees indicated times to the most recent common ancestors of 34–46 years (before 2008) depending on the RNA segment and the method of tree inference.

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

Phylogenetic Relations of Rhizoplaca Zopf. from Anatolia Inferred from ITS Sequence Data

2006 ◽  
Vol 61 (5-6) ◽  
pp. 405-412 ◽  
Author(s):  
Demet Cansaran ◽  
Sümer Aras ◽  
İrfan Kandemir ◽  
Gökhan Halıcı
Keyword(s):  
Genetic Variability ◽  
Phylogenetic Tree ◽  
Sequence Data ◽  
Volcanic Rocks ◽  
Morphological Characteristics ◽  
Its Rdna ◽  
Its Sequence ◽  
Phylogenetic Relations ◽  
Rdna Sequences

Like many lichen-forming fungi, species of the genus Rhizoplaca have wide geographical distributions, but studies of their genetic variability are limited. The information about the ITS rDNA sequences of three species of Rhizoplaca from Anatolia was generated and aligned with other species from other countries and also with the data belonging to Lecanora species. The examined species were collected from the volcanic rocks of Mount Erciyes which is located in the middle of Anatolia (Turkey). The sequence data aligned with eight other samples of Rhizoplaca and six different species of Lecanora were obtained from GenBank. The results support the concept maintained by Arup and Grube (2000) that Rhizoplaca may not be a genus separate from Lecanora. According to the phylogenetic tree, Rhizoplaca melanopthalma from Turkey with two different samples of R. melanopthalma from Arizona (AF159929, AF159934) and a sample from Austria formed a group under the same branch. R. peltata and R. chrysoleuca samples from Anatolia located in two other branches of the tree formed sister groups with the samples of the same species from different countries. Although R. peltata remained on the same branch with other samples of the same species from other countries it was placed in a different branch within the group. When the three species from Anatolia were considered alone, it was noticed that Rhizoplaca melanopthalma and Rhizoplaca peltata are phylogenetically closer to each other than Rhizoplaca chrysoleuca; the morphological characteristics also support this result.

scholarly journals Characterization of Coolia spp. (Gonyaucales, Dinophyceae) from Southern Tunisia: first record of Coolia malayensis in the Mediterranean Sea

ALGAE ◽  
2021 ◽  
Vol 36 (3) ◽  
pp. 175-193
Author(s):  
Moufida Abdennadher ◽  
Amel Bellaaj Zouari ◽  
Walid Medhioub ◽  
Antonella Penna ◽  
Asma Hamza
Keyword(s):  
Electron Microscopy ◽  
Mediterranean Sea ◽  
Phylogenetic Trees ◽  
Eastern Mediterranean ◽  
First Record ◽  
Morphological Characterization ◽  
Mucus Production ◽  
Rdna Sequences ◽  
The Mediterranean ◽  
Morphological Differences

This study provides the first report of the presence of Coolia malayensis in the Mediterranean Sea, co-occurring with C. monotis. Isolated strains from the Gulf of Gabès, Tunisia (South-eastern Mediterranean) were identified by morphological characterization and phylogenetic analysis. Examination by light and scanning electron microscopy revealed no significant morphological differences between the Tunisian isolates and other geographically distant strains of C. monotis and C. malayensis. Phylogenetic trees based on ITS1-5.8S-ITS2 and D1‒D3/28S rDNA sequences showed that C. monotis strains clustered with others from the Mediterranean and Atlantic whereas the C. malayensis isolate branched with isolates from the Pacific and the Atlantic, therefore revealing no geographical trend among C. monotis and C. malayensis populations. Ultrastructural analyses by transmission electron microscopy revealed the presence of numerous vesicles containing spirally coiled fibers in both C. malayensis and C. monotis cells, which we speculate to be involved in mucus production.

Phylogenomics of orchids and their mycorrhizal fungi : trees, diversity, and the pursuit of symbiosis

2019 ◽  
Author(s):  
◽  
Sarah Unruh
Keyword(s):  
Mycorrhizal Fungi ◽  
Phylogenetic Trees ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Mycorrhizal Symbiosis ◽  
Sequencing Data ◽  
Phylogenetic Structure ◽  
University Of Missouri ◽  
Fungal Symbiosis

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Phylogenetic trees show us how organisms are related and provide frameworks for studying and testing evolutionary hypotheses. To better understand the evolution of orchids and their mycorrhizal fungi, I used high-throughput sequencing data and bioinformatic analyses, to build phylogenetic hypotheses. In Chapter 2, I used transcriptome sequences to both build a phylogeny of the slipper orchid genera and to confirm the placement of a polyploidy event at the base of the orchid family. Polyploidy is hypothesized to be a strong driver of evolution and a source of unique traits so confirming this event leads us closer to explaining extant orchid diversity. The list of orthologous genes generated from this study will provide a less expensive and more powerful method for researchers examining the evolutionary relationships in Orchidaceae. In Chapter 3, I generated genomic sequence data for 32 fungal isolates that were collected from orchids across North America. I inferred the first multi-locus nuclear phylogenetic tree for these fungal clades. The phylogenetic structure of these fungi will improve the taxonomy of these clades by providing evidence for new species and for revising problematic species designations. A robust taxonomy is necessary for studying the role of fungi in the orchid mycorrhizal symbiosis. In chapter 4 I summarize my work and outline the future directions of my lab at Illinois College including addressing the remaining aims of my Community Sequencing Proposal with the Joint Genome Institute by analyzing the 15 fungal reference genomes I generated during my PhD. Together these chapters are the start of a life-long research project into the evolution and function of the orchid/fungal symbiosis.

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