Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species

Polynoidae Kinberg, 1856 has five branchiate genera: Branchipolynoe Pettibone, 1984, Branchinotogluma Pettibone, 1985, Branchiplicatus Pettibone, 1985, Peinaleopolynoe Desbruyères & Laubier, 1988, and Thermopolynoe Miura, 1994, all native to deep-sea, chemosynthetic-based habitats. Of these, Peinaleopolynoe has two accepted species; Peinaleopolynoe sillardi Desbruyères & Laubier, 1988 (Atlantic Ocean) and Peinaleopolynoe santacatalina Pettibone, 1993 (East Pacific Ocean). The goal of this study was to assess the phylogenetic position of Peinaleopolynoe, utilizing DNA sequences from a broad sampling of deep-sea polynoids. Representatives from all five branchiate genera were included, several species of which were sampled from near the type localities; Branchinotogluma sandersi Pettibone, 1985 from the Galápagos Rift (E/V “Nautilus”); Peinaleopolynoe sillardi from organic remains in the Atlantic Ocean; Peinaleopolynoe santacatalina from a whalefall off southern California (R/V “Western Flyer”) and Thermopolynoe branchiata Miura, 1994 from Lau Back-Arc Basin in the western Pacific (R/V “Melville”). Phylogenetic analyses were conducted using mitochondrial (COI, 16S rRNA, and CytB) and nuclear (18S rRNA, 28S rRNA, and H3) genes. The analyses revealed four new Peinaleopolynoe species from the Pacific Ocean that are formally described here: Peinaleopolynoe orphanae Hatch & Rouse, sp. nov., type locality Pescadero Basin in the Gulf of California, Mexico (R/V “Western Flyer”); Peinaleopolynoe elvisi Hatch & Rouse, sp. nov. and Peinaleopolynoe goffrediae Hatch & Rouse, sp. nov., both with a type locality in Monterey Canyon off California (R/V “Western Flyer”) and Peinaleopolynoe mineoi Hatch & Rouse, sp. nov. from Costa Rica methane seeps (R/V “Falkor”). In addition to DNA sequence data, the monophyly of Peinaleopolynoe is supported by the presence of ventral papillae on segments 12–15. The results also demonstrated the paraphyly of Branchinotogluma and Lepidonotopodium Pettibone, 1983 and taxonomic revision of these genera is required. We apply the subfamily name Lepidonotopodinae Pettibone 1983, for the clade comprised of Branchipolynoe, Branchinotogluma, Bathykurila, Branchiplicatus, Lepidonotopodium, Levensteiniella Pettibone, 1985, Thermopolynoe, and Peinaleopolynoe.

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Molecular evolution and diversification of the vestimentiferan tube worms

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315400032987 ◽

1993 ◽

Vol 73 (2) ◽

pp. 437-452 ◽

Cited By ~ 40

Author(s):

Nic A. Williams ◽

David R. Dixon ◽

Eve C. Southward ◽

Peter W. H. Holland

Keyword(s):

Dna Sequences ◽

Deep Sea ◽

Marine Invertebrates ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Dna Sequence Data ◽

Evolutionary Diversification ◽

Tube Worms ◽

Eastern Atlantic Ocean ◽

Phylogenetic Affinities

The Vestimentifera, or deep-sea tube worms, comprise an ecologically and anatomically unusual group of marine invertebrates, with poorly understood biogeography, ecology, phylogenetic affinities and evolutionary radiation. To gain insight into evolutionary diversification within the group, we have used a molecular biological approach. We report the cloning of a region of 28S ribosomal DNA from representatives of five vestimentiferan genera plus, for comparison, a polychaete and a perviate pogonophore. Phylogenetic analyses using these DNA sequences confirm thatRidgeiaandTevniaare closely related genera. The analyses also lead us to propose the hypothesis that the earliest vestimentiferan lineage to diverge gave rise to the genusLamellibrachiaonly. In addition, our comparative DNA sequence data now provide a means to use molecular methods for identification of deep-sea tube worms; we employed this approach to demonstrate that the first vestimentiferan specimen from the eastern Atlantic Ocean belongs to the genusLamellibrachia. DNA-based identification should have wide applications in the study of vestimentiferan biogeography and ecology.

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Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽

10.1515/mammalia-2017-0081 ◽

2019 ◽

Vol 83 (2) ◽

pp. 180-189 ◽

Cited By ~ 2

Author(s):

Adam W. Ferguson ◽

Houssein R. Roble ◽

Molly M. McDonough

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Alternative Hypothesis ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Sister Relationship ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Molecular Phylogenetic ◽

Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

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Morphology, genetic characterization and molecular phylogeny of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) from the endangered Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae)

Parasites & Vectors ◽

10.1186/s13071-020-04430-6 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Yi-Fan Cao ◽

Hui-Xia Chen ◽

Yang Li ◽

Dang-Wei Zhou ◽

Shi-Long Chen ◽

...

Keyword(s):

New Species ◽

Ribosomal Dna ◽

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Small Subunit ◽

Sister Relationship ◽

Tibetan Antelope ◽

A New Species

Abstract Background The Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae) is an endangered species of mammal endemic to the Qinghai-Tibetan Plateau. Parasites and parasitic diseases are considered to be important threats in the conservation of the Tibetan antelope. However, our present knowledge of the composition of the parasites of the Tibetan antelope remains limited. Methods Large numbers of nematode parasites were collected from a dead Tibetan antelope. The morphology of these nematode specimens was observed using light and scanning electron microscopy. The nuclear and mitochondrial DNA sequences, i.e. small subunit ribosomal DNA (18S), large subunit ribosomal DNA (28S), internal transcribed spacer (ITS) and cytochrome c oxidase subunit 1 (cox1), were amplified and sequenced for molecular identification. Moreover, phylogenetic analyses were performed using maximum likelihood (ML) inference based on 28S and 18S + 28S + cox1 sequence data, respectively, in order to clarify the systematic status of these nematodes. Results Integrated morphological and genetic evidence reveals these nematode specimens to be a new species of pinworm Skrjabinema longicaudatum (Oxyurida: Oxyuridae). There was no intraspecific nucleotide variation between different individuals of S. longicaudatum n. sp. in the partial 18S, 28S, ITS and cox1 sequences. However, a high level of nucleotide divergence was revealed between the new species and its congeners in 28S (8.36%) and ITS (20.3–23.7%) regions, respectively. Molecular phylogenetic results suggest that the genus Skrjabinema should belong to the subfamily Oxyurinae (Oxyuroidea: Oxyuridae), instead of the subfamily Syphaciidae or Skrjabinemiinae in the traditional classification, as it formed a sister relationship to the genus Oxyuris. Conclusions A new species of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) is described. Skrjabinema longicaudatum n. sp. represents the first species of Oxyurida (pinworm) and the fourth nematode species reported from the Tibetan antelope. Our results contribute to the knowledge of the species diversity of parasites from the Tibetan antelope, and clarify the systematic position of the genus Skrjabinema.

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Strelitziana sarbhoyi sp. nov. (Strelitzianaceae, Chaetothyriales), from North-Western Himalayas, India, described based on morphology and molecular phylogeny

Phytotaxa ◽

10.11646/phytotaxa.427.1.6 ◽

2019 ◽

Vol 427 (1) ◽

pp. 51-59

Author(s):

SHIWALI RANA ◽

SANJAY KUMAR SINGH ◽

PARAS NATH SINGH

Keyword(s):

Phylogenetic Tree ◽

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Culture Collection ◽

Fungal Culture ◽

Western Himalayas ◽

Holotype Specimen ◽

North Western

Strelitziana sarbhoyi is established as a new species to accommodate a phylloplane fungus isolated from Mallotus philippensis collected from Kangra region of North-Western Himalayas, Himachal Pradesh. The identity of the fungus is confirmed based on the asexual-morphs, cultural characteristics and phylogenetic analyses of the internal transcribed spacer (ITS) rDNA and partial nuclear ribosomal 28S large subunit (LSU) sequence data. The placement of S. sarbhoyi in the phylogenetic tree was determined based on DNA sequences from authenticated isolates of Strelitziana. Strelitziana sarbhoyi shows nearly 94% similarity with other known species of Strelitziana. Area description is provided for the proposed taxon along with microscopic images, and a phylogenetic tree. This is probably the first report of Strelitziana from India. Holotype specimen (dried voucher culture) is deposited in the Ajrekar Mycological Herbarium (AMH), and an ex-type culture is deposited in National Fungal Culture Collection of India (NFCCI).

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Phylogenetic position of Sphaerospora testicularis and Latyspora scomberomori n. gen. n. sp. (Myxozoa) within the marine urinary clade

Parasitology ◽

10.1017/s0031182010001381 ◽

2010 ◽

Vol 138 (3) ◽

pp. 381-393 ◽

Cited By ~ 24

Author(s):

PAVLA BARTOŠOVÁ ◽

MARK A. FREEMAN ◽

HIROSHI YOKOYAMA ◽

MONICA CAFFARA ◽

IVAN FIALA

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Dicentrarchus Labrax ◽

Sensu Stricto ◽

Phylogenetic Position ◽

Species Cluster ◽

The Family ◽

Sutural Line ◽

Taxonomic Changes

SUMMARYAn amendment of the family Sinuolineidae (Myxosporea) is proposed in order to include a newly described genus Latyspora n. gen. The type species Latyspora scomberomori n. gen. n. sp. is a coelozoic parasite in the kidney tubules of Scomberomorus guttatus. In addition to the morphological and molecular characterization of L. scomberomori n. gen. n. sp., we also present novel SSU rDNA data on Sphaerospora testicularis, a serious parasite of Dicentrarchus labrax. Performed phylogenetic analyses revealed that both species cluster within the marine urinary clade encompassing the representatives with a shared insertion within their V4 SSU rRNA region and grouping according to the shape of their spores’ sutural line and their similar tissue tropism in the host. Sphaerospora testicularis is the closest relative to Parvicapsula minibicornis within the Parvicapsula subclade and L. scomberomori n. gen. n. sp. is the basal species of the Zschokkella subclade. The phylogenetic position of S. testicularis, outwith the basal Sphaerospora sensu stricto clade, and its morphology suggest it being a non-typical Sphaerospora. The sequence data provided on S. testicularis can help in future revisions of the strongly polyphyletic genus Sphaerospora. We recommend re-sequencing of several sphaerosporids as an essential step before such taxonomic changes are accomplished.

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A new and endangered species of Iochroma (Solanaceae) from the cloud forests of central Peru and its phylogenetic position in Iochrominae

Phytotaxa ◽

10.11646/phytotaxa.227.2.4 ◽

2015 ◽

Vol 227 (2) ◽

pp. 147 ◽

Cited By ~ 4

Author(s):

Marco Antonio Cueva Manchego ◽

STACEY DEWITT SMITH ◽

SEGUNDO LEIVA GONZÁLES

Keyword(s):

New Species ◽

Endangered Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Phylogenetic Position ◽

Cloud Forests ◽

Dna Sequence Data ◽

A New Species ◽

Iucn Criteria

Iochroma amicorum M. Cueva, S. D. Sm. & S. Leiva (Solanaceae), a new species from cloud forests of Central Peru, is described and illustrated. Phylogenetic analyses of DNA sequence data suggest that Iochroma amicorum is closely related to I. nitidum, I. umbellatum, I. grandiflorum and I. tingoanum, which collectively form the “U” clade of Iochrominae. Certain morphological characteristics of calyx and corolla as well as the type of habitat appear to be common in species of this clade. Iochroma amicorum is easily distinguished from other members of the “U” clade by its campanulate or funnel-shaped corolla with short and slightly reflexed lobes, the presence of an expanded stapet at the point of filament insertion with short lateral extensions united to the corolla, and its globose usually white fruits with tinges of purple at the base. Distribution, phenology and are discussed together with the position of the new species in Iochrominae. Iochroma amicorum is assessed as Endangered according to IUCN criteria B1ab (i, iii)

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Morphology, Morphogenesis, and Molecular Phylogeny of a New Freshwater Ciliate, Quadristicha subtropica n. sp. (Ciliophora, Hypotrichia)

Frontiers in Microbiology ◽

10.3389/fmicb.2021.705826 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chen Shao ◽

Qi Gao ◽

Alan Warren ◽

Jingyi Wang

Keyword(s):

Sequence Data ◽

Southern China ◽

Phylogenetic Analyses ◽

Small Subunit ◽

Systematic Position ◽

Phylogenetic Position ◽

Dna Sequence Data ◽

Freshwater Pond ◽

Small Subunit Ribosomal Dna

The morphology and the regulation of cortical pattern associated with the cell size, division, and phylogenetic position of a new hypotrichous ciliate, Quadristicha subtropica n. sp. collected from a freshwater pond in southern China, were investigated. Quadristicha subtropica n. sp. is characterized as follows: size in vivo 60–115 μm × 25–45 μm; 19–21 adoral membranelles; buccal cirrus near anterior end of endoral and paroral; cirrus IV/3 at about level of buccal vertex; right marginal row begins ahead of buccal vertex; 11–16 right and 12–19 left marginal cirri; and dorsal cilia about 5 μm long. The basic morphogenetic process in Q. subtropica n. sp. is consistent with that of the type species, Quadristicha setigera. Phylogenetic analyses based on small subunit ribosomal DNA sequence data reveal that the systematic position of Q. subtropica n. sp. is rather unstable with low support values across the tree and the genus Quadristicha is not monophyletic.

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Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽

10.12688/f1000research.23635.2 ◽

2020 ◽

Vol 9 ◽

pp. 339 ◽

Cited By ~ 1

Author(s):

Tshifhiwa G. Matumba ◽

Jody Oliver ◽

Nigel P. Barker ◽

Christopher D. McQuaid ◽

Peter R. Teske

Keyword(s):

Dna Barcoding ◽

Dna Sequences ◽

Sequence Data ◽

Mitochondrial Gene ◽

Population Expansion ◽

Species Level ◽

Molecular Dating ◽

Coi Gene ◽

28S Rrna ◽

Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

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Morphology, genetic characterization and molecular phylogeny of pinworm Skrjabinema longicaudatum sp. n. (Oxyurida: Oxyuridae) from the endangered Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae)

10.21203/rs.3.rs-68446/v1 ◽

2020 ◽

Author(s):

Yi-Fan Cao ◽

Hui-Xia Chen ◽

Yang Li ◽

Dang-Wei Zhou ◽

Shi-Long Chen ◽

...

Keyword(s):

New Species ◽

Ribosomal Dna ◽

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Nematode Species ◽

Sister Relationship ◽

Tibetan Antelope ◽

A New Species ◽

Cox 1

Abstract Background The Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae) is an endangered and endemic species of mammal to the Qinghai-Tibetan Plateau. Parasites and their caused parasitic diseases are considered to be important threats in the conservation of the Tibetan antelope. However, our present knowledge of the composition of the parasites from the Tibetan antelope remains limited. Methods Large numbers of nematode parasites were collected from a dead Tibetan antelope. The morphology of these nematode specimens were observed using light and scanning electron microscopy. The nuclear and mitochondrial DNA sequences [i.e. small ribosomal DNA (18S), large ribosomal DNA (28S), internal transcribed spacer (ITS) and cytochrome c oxidase subunit 1 ( cox 1)] were amplified and sequenced for molecular identification. Moreover, phylogenetic analyses were performed using maximum likelihood (ML) inference based on 28S and 18S + 28S + cox 1 sequence data, respectively, in order to clarify the systematic status of these nematodes. Results Integrated morphological and genetic evidence reveals these nematode specimens to be a new species of pinworm Skrjabinema longicaudatum sp. n. (Oxyurida: Oxyuridae). There is no intraspecific nucleotide variation found between different individuals of S. longicaudatum sp. n. in the partial 18S, 28S, ITS and cox 1 sequences. However, the high level of nucleotide divergence was revealed between the new species and its congeners in 28S (8.36%) and ITS (20.3–23.7%) regions, respectively. Molecular phylogenetic results supported that the genus Skrjabinema should belong to the subfamily Oxyurinae (Oxyuroidea: Oxyuridae), instead of the subfamily Syphaciidae or Skrjabinemiinae in the traditional classification, which formed a sister relationship to the genus Oxyuris . Conclusions A new species of pinworm Skrjabinema longicaudatum sp. n. (Oxyurida: Oxyuridae) was described. Skrjabinema longicaudatum sp. n. represents the first species of Oxyurida (pinworm) and the fourth nematode species reported from the Tibetan antelope. Our results contribute to our knowledge on the species diversity of parasites from the Tibetan antelope, and also clarified the systematic position of the genus Skrjabinema .

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Two new asexual genera and six new asexual species in the family Microthyriaceae (Dothideomycetes, Ascomycota) from China

MycoKeys ◽

10.3897/mycokeys.85.70829 ◽

2021 ◽

Vol 85 ◽

pp. 1-30

Author(s):

Min Qiao ◽

Hua Zheng ◽

Ji-Shu Guo ◽

Rafael F. Castañeda-Ruiz ◽

Jian-Ping Xu ◽

...

Keyword(s):

New Taxa ◽

Dna Sequences ◽

Sequence Data ◽

Southern China ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Aquatic Hyphomycetes ◽

Internal Transcribed Spacers ◽

The Family

The family Microthyriaceae is represented by relatively few mycelial cultures and DNA sequences; as a result, the taxonomy and classification of this group of organisms remain poorly understood. During the investigation of the diversity of aquatic hyphomycetes from southern China, several isolates were collected. These isolates were cultured and sequenced and a BLAST search of its LSU sequences against data in GenBank revealed that the closest related taxa are in the genus Microthyrium. Phylogenetic analyses, based on the combined sequence data from the internal transcribed spacers (ITS) and the large subunit (LSU), revealed that these isolates represent eight new taxa in Microthyriaceae, including two new genera, Antidactylariagen. nov. and Isthmomycesgen. nov. and six new species, Antidactylaria minifimbriatasp. nov., Isthmomyces oxysporussp. nov., I. dissimilissp. nov., I. macrosporussp. nov., Triscelophorus anisopterioideussp. nov. and T. sinensissp. nov. These new taxa are described, illustrated for their morphologies and compared with similar taxa. In addition, two new combinations are proposed in this family.

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