scholarly journals Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera

2020 ◽  
Vol 12 (3) ◽  
pp. 203-209
Author(s):  
Eiichi Shoguchi ◽  
Yuki Yoshioka ◽  
Chuya Shinzato ◽  
Asuka Arimoto ◽  
Debashish Bhattacharya ◽  
...  
Keyword(s):  
Rna Editing ◽  
Phylogenetic Analyses ◽  
Snp Analysis ◽  
Ryukyu Archipelago ◽  
The North ◽  
Acropora Digitifera ◽  
Organelle Genomes ◽  
Molecular Phylogenetic ◽  
Symbiotic Dinoflagellates ◽  
Organelle Genes

Abstract In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates.

scholarly journals Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

2021 ◽  
pp. 1-28
Author(s):  
Yoshimasa Kumekawa ◽  
Haruka Fujimoto ◽  
Osamu Miura ◽  
Ryo Arakawa ◽  
Jun Yokoyama ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Ryukyu Archipelago ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

A revision of the Leptogium saturninum group in North America

2016 ◽  
Vol 48 (5) ◽  
pp. 387-421 ◽  
Author(s):  
Daphne F. STONE ◽  
James W. HINDS ◽  
Frances L. ANDERSON ◽  
James C. LENDEMER
Keyword(s):  
North American ◽  
Morphological Study ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Lower Surface ◽  
Molecular Data ◽  
The North ◽  
Molecular Phylogenetic ◽  
Nrits Sequence

AbstractA revision of the North American members of the Leptogium saturninum group (i.e. species with long lower-surface hairs, isidia, and usually smooth upper surface) is presented based on molecular phylogenetic analyses of mtSSU and nrITS sequence data, together with an extensive morphological study. Three species supported by both molecular and morphological characteristics are recognized: L. acadiense sp. nov. (distinguished by granular saturninum-type isidia, medulla composed of irregularly arranged or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type isidia and medulla composed of loosely intertwined hyphae). One species supported by morphological characteristics, but for which no molecular data could be generated, is also recognized: L. compactum sp. nov. (distinguished by hirsutum-type isidia and medulla composed of tightly packed hyphae). Finally, L. saturninum (distinguished by granular saturninum-type isidia and medulla composed of perpendicular and parallel hyphae) is supported by morphological characteristics but molecular data from geographically diverse populations, including those near the type locality, indicate that the morphologically defined species is paraphyletic. Leptogium burnetiae is excluded from North American based on morphological study of the type. The species are described and illustrated in detail, and are distinguished morphologically by their isidium development, morphology of mature isidia, and pattern of hyphae in the medulla in transverse sections near lobe margins. A key to the members of the L. saturninum group and related species is also presented.

New records of Serpulidae (Annelida, Polychaeta) from hydrothermal vents of North Fiji, Pacific Ocean

Zootaxa ◽  
2010 ◽  
Vol 2389 (1) ◽  
pp. 57 ◽  
Author(s):  
ELENA K. KUPRIYANOVA ◽  
EIJIROH NISHI ◽  
MASARU KAWATO ◽  
YOSHIHIRO FUJIWARA
Keyword(s):  
Ribosomal Rna ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
New Records ◽  
Phylogenetic Analyses ◽  
Suspension Feeding ◽  
North East ◽  
The North ◽  
East Pacific ◽  
Molecular Phylogenetic

Serpulidae are sessile suspension-feeding annelids commonly found in the periphery of hydrothermal vents, but up to now only two species, Laminatubus alvini and Protis hydrothermica had been described from such communities. This paper reports two additional serpulid species, collected in 2005 from the North Fiji hydrothermal vent area, identified as Hyalopomatus mironovi and Protis sp. The former has originally been described from the Kurile-Kamchatka Trench and the later recorded from the North-East Pacific. The latter species is similar to Protis hydrothermica, but lacks special finand-blade collar chaetae typical of this genus. Illustrated re-descriptions of the two species have been supplemented by molecular sequences (18S ribosomal RNA). Molecular phylogenetic analyses show that Hyalopomatus mironovi and Protis sp. are sister species of Laminatubus alvini and Protis hydrothermica, respectively.

A new amphibious species of the genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae) from the Ryukyu Archipelago and Taiwan

Zootaxa ◽  
2021 ◽  
Vol 4952 (3) ◽  
pp. 465-494
Author(s):  
SHO TSUKAMOTO ◽  
SHIMPEI F. HIRUTA ◽  
KATSUYUKI EGUCHI ◽  
JHIH-RONG LIAO ◽  
SATOSHI SHIMANO
Keyword(s):  
Phylogenetic Analyses ◽  
Rrna Genes ◽  
Valid Species ◽  
28S Rrna ◽  
Ryukyu Archipelago ◽  
Morphological Examination ◽  
Mitochondrial Coi ◽  
Molecular Phylogenetic ◽  
East And Southeast Asia ◽  
18S Rrna Genes

In Japan and Taiwan, five valid species of the genus Scolopendra Linnaeus, 1758 have been described: S. morsitans Linnaeus, 1758, S. subspinipes Leach, 1816, S. mutilans Koch, 1878, S. japonica Koch, 1878, and S. multidens Newport, 1844. Recently, an undetermined species was found in the Ryukyu Archipelago and Taiwan. Using molecular phylogenetic analyses with mitochondrial COI and 16S rRNA and nuclear 28S rRNA and 18S rRNA genes as well as conventional morphological examination, we successfully discriminated this sixth species as an independent lineage from S. subspinipes, S. mutilans, and other named congeners from East and Southeast Asia. Therefore, the species was described as S. alcyona Tsukamoto & Shimano, sp. nov. Several situational evidences suggest that this species prefers streamside environments and exhibits amphibious behavior. 

A new species of Acantothereva Séguy, 1935, from Tunisia (Diptera: Therevidae: Therevinae): taxonomic consequences and phylogenetic implications

Zootaxa ◽  
2009 ◽  
Vol 2155 (1) ◽  
pp. 28-36 ◽  
Author(s):  
KEVIN C. HOLSTON
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
North African ◽  
The North ◽  
Interspecific Differences ◽  
Close Phylogenetic Relationship ◽  
Phylogenetic Implications ◽  
Molecular Phylogenetic ◽  
A New Species ◽  
African Genus

A new Tunisian species of Acantothereva Séguy is described, reducing several diagnostic characters for this North African genus to interspecific differences among the three included species. An expanded vertex and frons were formerly considered diagnostic for the genus, but the new species, A. oblata, sp. nov., has a vertex lower than the dorsal eye margin and a non-dilated ocellar tubercle. Previously recognized male genitalic characters, however, support the hypothesis that Acantothereva is a monophyletic group. The ability to recognize Acantothereva using external characters is marginally reduced with respect to therevine genera due to the inclusion of the new species, notably relative to Neotherevella Lyneborg. The apparent close phylogenetic relationship among Acantothereva, Acrosathe Irwin & Lyneborg, Irwiniella Lyneborg, and Neotherevella Lyneborg species are discussed herein, based on recent molecular phylogenetic analyses and the morphology of the Tunisian Acantothereva species. A key to the North African therevine genera is included; head and genitalia illustrations and a key to the three Acantothereva species are also presented.

Disentangling the evolutionary and biogeographical history of the freshwater fish trematode genus Creptotrema (Digenea: Allocreadiidae) using an integrative taxonomy approach: the case of Creptotrema agonostomi in Middle American mountain mullets

2020 ◽  
Vol 94 ◽  
Author(s):  
G. Pérez-Ponce de León ◽  
A.L. Sereno-Uribe ◽  
M. García-Varela ◽  
B. Mendoza-Garfias ◽  
D.I. Hernández-Mena ◽  
...  
Keyword(s):  
New York ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
New York State ◽  
Integrative Taxonomy ◽  
Similar Species ◽  
The North ◽  
Middle America ◽  
Molecular Phylogenetic ◽  
Three New Species

Abstract Species of the allocreadiid genus Creptotrema are parasites of freshwater fishes in the Americas. Species in the genus possess one pair of muscular oral lobes on the oral sucker. Currently, the genus contains eight species, six distributed in South America, one in Middle America and one in North America. Genetic data are only available for the North American species, Creptotrema funduli, a parasite of fundulids originally described from Oneida Lake, New York State. In this study, we obtained 28S ribosomal DNA sequences of trematodes morphologically similar to Creptotrema agonostomi from the mountain mullet, Dajaus monticola, across a wide geographical range in Middle America. Our molecular phylogenetic analyses showed that (1) the genus Creptotrema, as currently conceived, is not monophyletic; (2) the allocreadiids in mountain mullets should be re-allocated in the genus Pseudoparacreptotrema; and (3) the allocreadiid trematodes from D. monticola across Middle America represent four morphologically similar species, three of which can be distinguished genetically. These three new species are described herein using an integrative taxonomy approach. We contend that accurate estimates of species diversity and phylogenetic relationships among allocreadiids, and most likely other species of trematodes, necessarily require an integrative taxonomy approach that should consider at least DNA sequences and scanning electron microscopy.

scholarly journals Stolonifera from shallow waters in the north-western Pacific: a description of a new genus and two new species within the Arulidae (Anthozoa, Octocorallia)

ZooKeys ◽  
2018 ◽  
Vol 790 ◽  
pp. 1-19 ◽  
Author(s):  
Yee Wah Lau ◽  
Frank Robert Stokvis ◽  
Leendert Pieter van Ofwegen ◽  
James Davis Reimer
Keyword(s):  
New Species ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Shallow Waters ◽  
The North ◽  
The Family ◽  
Two New Species ◽  
Molecular Phylogenetic ◽  
Dongsha Atoll ◽  
North Western

A new genus and two new species of stoloniferous octocorals (Alcyonacea) within the family Arulidae are described based on specimens collected from Okinawa (Japan), Palau and Dongsha Atoll (Taiwan).Hanagen. n. is erected within Arulidae.Hanahanagasasp. n.is characterised by large spindle-like table-radiates andHanahanatabasp. n.is characterised by having ornamented rods. The distinction of these new taxa is also supported by molecular phylogenetic analyses. The support values resulting from maximum likelihood and Bayesian inference analyses for the genusHanaand new speciesH.hanagasaandH.hanatabaare 82/1.0, 97/1.0 and 61/0.98, respectively.Hanahanagasasp. n.andHanahanatabasp. n.are the first arulid records for Okinawa, Palau, and Dongsha Atoll, and represent species of the second genus within the family Arulidae.

scholarly journals Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America

2016 ◽  
Vol 12 (4) ◽  
pp. 20160062 ◽  
Author(s):  
Kieren J. Mitchell ◽  
Sarah C. Bray ◽  
Pere Bover ◽  
Leopoldo Soibelzon ◽  
Blaine W. Schubert ◽  
...  
Keyword(s):  
South America ◽  
North American ◽  
Convergent Evolution ◽  
Phylogenetic Analyses ◽  
Early Pleistocene ◽  
South American ◽  
The North ◽  
Molecular Phylogenetic ◽  
North And South America ◽  
North And South

The Tremarctinae are a subfamily of bears endemic to the New World, including two of the largest terrestrial mammalian carnivores that have ever lived: the giant, short-faced bears Arctodus simus from North America and Arctotherium angustidens from South America (greater than or equal to 1000 kg). Arctotherium angustidens became extinct during the Early Pleistocene, whereas Arctodus simus went extinct at the very end of the Pleistocene. The only living tremarctine is the spectacled bear ( Tremarctos ornatus ), a largely herbivorous bear that is today only found in South America. The relationships among the spectacled bears ( Tremarctos ), South American short-faced bears ( Arctotherium ) and North American short-faced bears ( Arctodus ) remain uncertain. In this study, we sequenced a mitochondrial genome from an Arctotherium femur preserved in a Chilean cave. Our molecular phylogenetic analyses revealed that the South American short-faced bears were more closely related to the extant South American spectacled bear than to the North American short-faced bears. This result suggests striking convergent evolution of giant forms in the two groups of short-faced bears ( Arctodus and Arctotherium ), potentially as an adaptation to dominate competition for megafaunal carcasses.

Antitropical distribution of Lobelia species (Campanulaceae) between the Ryukyu Archipelago of Japan and Oceania as indicated by molecular data

2012 ◽  
Vol 60 (5) ◽  
pp. 417 ◽  
Author(s):  
Goro Kokubugata ◽  
Koh Nakamura ◽  
Paul I. Forster ◽  
Yumiko Hirayama ◽  
Masatsugu Yokota
Keyword(s):  
New Zealand ◽  
Distribution Pattern ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Sister Species ◽  
Ryukyu Archipelago ◽  
Molecular Phylogenetic

We tested the antitropical distribution of Lobelia loochooensis, endemic to the Ryukyu Archipelago of Japan, and its putative sister species of the same section Hypsela in Oceania (Australia and New Zealand). Molecular phylogenetic analyses based on cpDNA sequences were conducted for 41 Lobelia species of 11 sections including all the species of sect. Hypsela investigated in Asia and Malesia and 32 species of 16 allied genera of family Campanulaceae, because the genus Lobelia is known to be polyphyletic. In the result, L. loochooensis and an Australian endemic L. fluviatilis formed a clade, and this clade was sister to a clade of four New Zealand endemics: L. carens, L. fatiscens, L. fugax and L. ionantha. These two clades were nested in a clade with two other Australian congeners. We conclude that: (1) the lineage of L. loochooensis and the five Lobelia species occurring in Oceania demonstrate an antitropical distribution pattern; and (2) L. loochooensis has likely originated from a dispersal event from Australia to the Ryukyu Archipelago.

scholarly journals Mycosphaerangium and Neomelanconium (Cenangiaceae) are closest relatives: phylogenetic relationships, morphology and a new species

2020 ◽  
Vol 19 (11) ◽  
pp. 1329-1352
Author(s):  
Hermann Voglmayr ◽  
Walter M. Jaklitsch ◽  
Salvador Tello
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Morphological Evidence ◽  
Lsu Rdna ◽  
The North ◽  
Molecular Phylogenetic ◽  
Fungal Associations ◽  
First Time ◽  
Ascospore Morphology ◽  
A New Species

Abstract Based on molecular phylogenetic analyses of a multigene matrix of partial nuSSU-ITS-LSU rDNA, RPB1, RPB2 and TEF1 sequences and by morphological evidence, the genus Mycosphaerangium is shown to be the closest relative of Neomelanconium, and confirmed to be a member of the Cenangiaceae (Leotiomycetes). While Mycosphaerangium and Neomelanconium share many traits like similar conidia, conidiogenesis, asci and ascospores, their apothecia differ particularly in excipular features and are therefore recognized as distinct genera. Mycosphaerangium tiliae, described from North America, is excluded from the genus but shown to represent the sexual morph of the European Neomelanconium gelatosporum, and it is therefore synonymized with the latter. Based on morphology, Neomelanconium deightonii is assumed to be congeneric with Neomelanconium gelatosporum, and it is lectotypified. Dermatea tetraspora and Phaeangium magnisporum, the basionyms of Mycosphaerangium tetrasporum and M. magnisporum, respectively, are lectotypified as well, and for M. tetrasporum, the asexual morph is recorded for the first time. Mycosphaerangium quercinum sp. nov. is described as a new species from various Quercus hosts in Europe, where it is shown to be widely distributed. It morphologically and ecologically closely resembles the North American M. tetrasporum, but differs in paraphysis and ascospore morphology and by croziers at its ascus base. The three accepted species of Mycosphaerangium and the two of Neomelanconium are described and illustrated. Mycosphaerangium magnisporum, M. quercinum and M. tetrasporum are recorded to be constantly associated with species of Coryneum, indicating a fungicolous habit, but no evidence for fungal associations has been found in Neomelanconium deightonii and N. gelatosporum.

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