A molecular phylogeny of the Palaearctic and Oriental members of the tribe Boarmiini (Lepidoptera : Geometridae : Ennominae)

Owing to the high species diversity and the lack of a modern revision, the phylogenetic relationships within the tribe Boarmiini remain largely unexplored. In this study, we reconstruct the first molecular phylogeny of the Palaearctic and Oriental members of Boarmiini, and infer the relationships among tribes within the ‘boarmiine’ lineage. One mitochondrial (COI) and four nuclear (EF-1α, CAD, RpS5, GAPDH) genes for 56 genera and 96 species of Boarmiini mostly from the Palaearctic and Oriental regions were included in the study. Analyses of Bayesian inference and maximum likelihood recovered largely congruent results. The monophyly of Boarmiini is supported by our results. Seven clades and seven subclades within Boarmiini were found. The molecular results coupled with morphological studies suggested the synonymisation of Zanclopera Warren, 1894, syn. nov. with Krananda Moore, 1868. The following new combinations are proposed: Krananda straminearia (Leech, 1897) (comb. nov.), Krananda falcata (Warren, 1894) (comb. nov.), and Krananda fulva (Yazaki, 1994) (comb. nov.). Our results also supported the monophyly of the ‘boarmiine’ lineage. Boarmiini were recovered as sister to the remaining taxa within the ‘boarmiine’ lineage, and Macariini were recovered as sister to Abraxini, Eutoeini and Cassymini.

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Molecular phylogeny of the butterfly tribe Baorini Doherty, 1886 (Hesperiidae, Hesperiinae) in China

Zootaxa ◽

10.11646/zootaxa.4565.1.8 ◽

2019 ◽

Vol 4565 (1) ◽

pp. 108 ◽

Cited By ~ 2

Author(s):

WEIBIN JIANG ◽

HAIYAN HE ◽

YUANYUAN LI ◽

YING WANG ◽

CHEN GE ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Maximum Likelihood ◽

Species Diversity ◽

Molecular Phylogeny ◽

Phylogenetic Relationships ◽

Mitochondrial Genes ◽

Nuclear Genes ◽

Large Group ◽

The Status

The butterfly tribe Baorini Doherty, 1886 is a large group of skippers. In this study, a total of 8 genera and 41 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2084 bp). Phylogenetic relationships and subdivision of this tribe were investigated and the status of the genera are discussed. Partitioned maximum likelihood analyses were performed based on the combined dataset. Our results suggest that the data are split into two well-supported clades in the phylogeny tree. This analysis also represents the most complete phylogenetic analysis of the tribe Baorini in China to date, and includes several genera and species that have been previously excluded from published phylogenies of this group.

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Systematic relationships of the Taeniapterini (Diptera: Micropezidae, Taeniapterinae)

Zootaxa ◽

10.11646/zootaxa.5004.2.6 ◽

2021 ◽

Vol 5004 (2) ◽

pp. 370-384

Author(s):

GUSTAVO BORGES FERRO ◽

JEFFREY H. SKEVINGTON ◽

STEPHEN A. MARSHALL ◽

SCOTT KELSO

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Cytochrome C ◽

16S Rrna ◽

Molecular Phylogeny ◽

Cytochrome C Oxidase ◽

28S Rrna ◽

Mitochondrial Cytochrome ◽

Oxidase Subunit ◽

Systematic Relationships

A molecular phylogeny for the Taeniapterinae is presented based on mitochondrial (cytochrome c oxidase subunit I, COI), ribosomal (16S rRNA and 28S rRNA) and nuclear (EF-1α and CAD) genes of 48 specimens including 40 species. Maximum likelihood and Bayesian inference were used to analyze the total concatenated dataset of 8769 bp. The results confirm that tribal classifications in Taeniapterinae are artificial and support the separation of Paragrallomyia Hendel and Taeniaptera sensu Ferro & Marshall (2020).

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A molecular phylogeny of the Grunts (Perciformes: Haemulidae) inferred using mitochondrial and nuclear genes

Zootaxa ◽

10.11646/zootaxa.2966.1.4 ◽

2011 ◽

Vol 2966 (1) ◽

pp. 37 ◽

Cited By ~ 11

Author(s):

MILLICENT D. SANCIANGCO ◽

LUIZ A. ROCHA ◽

KENT E. CARPENTER

Keyword(s):

Maximum Likelihood ◽

Molecular Phylogeny ◽

Strong Support ◽

Morphological Characters ◽

Cyt B ◽

Bayesian Analyses ◽

Mitochondrial Coi ◽

Outgroup Species ◽

Molecular Studies ◽

Upper Jaw

We infer a phylogeny of haemulid genera using mitochondrial COI and Cyt b genes and nuclear RAG1, SH3PX3, and Plagl2 genes from 56 haemulid species representing 18 genera of the expanded haemulids (including the former inermiids) and ten outgroup species. Results from maximum parsimony, maximum likelihood, and Bayesian analyses show strong support for a monophyletic Haemulidae with the inclusion of Emmelichthyops atlanticus. The former inermiids did not form a clade indicating that the highly protrusible upper jaw specialization to planktivory evolved more than once within Haemulidae. The subfamilies Haemulinae and Plectorhinchinae, currently diagnosed by eight morphological characters, most notably the number of chin pores and the origin of the retractor dorsalis, are also recovered from these analyses with the Haemulinae sister to the Plectorhinchinae. Plectorhinchus is monophyletic only with the inclusion of Diagramma. Within the Haemulinae, Pomadasys and Conodon are polyphyletic. In addition, Anisotremus is monophyletic only with the inclusion of Genyatremus and Conodon nobilis, and Haemulon is monophyletic only with the inclusion of Xenistius. These results suggest that further morphological and molecular studies are needed to revise the limits of several haemulid genera.

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The phylogenetic relationships of Paramesotriton (Caudata: Salamandridae) based on partial mitochondrial DNA gene sequences

Zootaxa ◽

10.11646/zootaxa.3150.1.3 ◽

2012 ◽

Vol 3150 (1) ◽

pp. 59

Author(s):

XIAOMING GU ◽

HUI WANG ◽

RONGRONG CHEN ◽

YINGZHOU TIAN ◽

SONG LI

Keyword(s):

Mitochondrial Dna ◽

Bayesian Inference ◽

Maximum Likelihood ◽

16S Rdna ◽

Phylogenetic Relationships ◽

Maximum Parsimony ◽

Mitochondrial Gene ◽

Sister Group ◽

Species Group ◽

Close Phylogenetic Relationship

We examined phylogenetic relationships among newst of the genus Paramesotriton using partial mitochondrial gene se-quences, including the ND2-tRNATyr region (1415 bp) and the 12S rDNA-tRNAVal -16S rDNA region (1774 bp), from 42individuals of 10 recognized Paramesotriton species and outgroups by Bayesian inference (BI), Maximum likelihood(ML) and Maximum Parsimony (MP) methods. We found that, (1) Laotriton laoensis is the sister group of Paramesotri-ton, (2) the genus Paramesotriton is monophyletic, composed of either the P. caudopunctatus species group and the P.chinensis species group, or the subgenera Allomesotriton and Paramesotriton (3) P. longliensis and P. zhijinensis shouldbe placed in the P. caudopunctatus species group or subgenus Allomesotriton; (4) P. fuzhongensis is not a junior synonym of P. chinensis, and there is a close phylogenetic relationship between P. fuzhongensis and P. guangxiensis.

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Revisiting the phylogeny and taxonomy of Osmanthus (Oleaceae) including description of the new genus Chengiodendron

Phytotaxa ◽

10.11646/phytotaxa.436.3.6 ◽

2020 ◽

Vol 436 (3) ◽

pp. 283-292 ◽

Cited By ~ 1

Author(s):

YONG-FU LI ◽

MIN ZHANG ◽

XIAN-RONG WANG ◽

STEVEN PAUL SYLVESTER ◽

QI-BAI XIANG ◽

...

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Phylogenetic Relationships ◽

Maximum Parsimony ◽

New Genus ◽

Morphological Character ◽

Strong Support ◽

Its Region ◽

Phylogenetic Placement ◽

Morphological Patterns

Osmanthus (Oleaceae) is considered one of the most confusing genera with regards to circumscription and phylogenetic placement of taxa within the subtribe Oleinae of Oleaceae, with controversies mainly focused on the attribution of section Leiolea. In the present study, we analyzed 71 samples that represent the broad taxonomic, biogeographic, and morphological patterns in the subtribe Oleinae. Based on concatenation of four plastid genes (trnL-F, trnT-L, trnS-G, and matK) and comparison with the ITS region, Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenies were inferred. Morphological character traits and geographical distributions of taxa were also studied. These results provide strong support for the segregation of the Leiolea clade (Osmanthus marginatus, O. matsumuranus and O. minor) of sect. Leiolea from Osmanthus. Therefore, the Leiolea clade is instated as the new genus Chengiodendron, with a taxonomic treatment provided. This study provides a clearer understanding of the phylogenetic relationships of genera in the subtribe Oleinae.

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High species diversity of the soft coral family Xeniidae (Octocorallia, Alcyonacea) in the temperate region of Japan revealed by morphological and molecular analyses

ZooKeys ◽

10.3897/zookeys.862.31979 ◽

2019 ◽

Vol 862 ◽

pp. 1-22 ◽

Cited By ~ 1

Author(s):

Tatsuki Koido ◽

Yukimitsu Imahara ◽

Hironobu Fukami

Keyword(s):

Species Diversity ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Soft Coral ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Temperate Region ◽

High Species Diversity ◽

Molecular Phylogenetic ◽

Traditional Taxonomy

The soft coral family Xeniidae, commonly found in tropical and subtropical regions, consists of 20 genera and 162 species. To date, few studies on this family have been conducted in Japan, especially at higher latitudes. Although molecular phylogenetic analyses have recently been used to distinguish soft coral species, it is difficult to identify species and genera in this family due to the limited taxonomic indices and high morphological variation. In this study, we found a large Xeniidae community off the coast of Oshima Island (31°31.35'N, 131°24.27'E) at Miyazaki, Kyushu Island, located in the temperate region of Japan. The species composition and molecular phylogenetic relationships were investigated to uncover the species diversity of Xeniidae in this community. A total of 182 xeniid specimens were collected and identified to the species level, after which the samples were molecularly analyzed using a mitochondrial marker (ND2) and a nuclear marker (ITS) to infer the phylogenetic relationships. A total of 14 xeniid species were identified, including five undescribed species from five genera (Anthelia, Heteroxenia, Sympodium, Xenia, and Yamazatum). Miyazaki was identified as having the highest xeniid species diversity in Japan. The molecular phylogenetic trees inferred from each marker recovered very similar topologies: four genera (Anthelia, Heteroxenia, Sympodium, and Yamazatum) were monophyletic, whereas one (Xenia) was polyphyletic. Thus, except for Xenia, the morphological characteristics used for traditional taxonomy well reflected the phylogeny of the Xeniidae at the genus level. On the other hand, our results show that further taxonomic revisions of Xenia are needed.

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Molecular Phylogeny of the Ant-Decapitating Flies, Genus Apocephalus Coquillett (Diptera: Phoridae)

Insect Systematics and Diversity ◽

10.1093/isd/ixy007 ◽

2018 ◽

Vol 2 (4) ◽

Cited By ~ 2

Author(s):

Brian V Brown ◽

Christine Hayes ◽

John M Hash ◽

Paul T Smith

Keyword(s):

Maximum Likelihood ◽

Molecular Phylogeny ◽

Phylogenetic Relationships ◽

Likelihood Methods ◽

Taxonomic Relationships ◽

Methods Of Analysis ◽

Maximum Likelihood Methods ◽

New Synonymy

Abstract The phylogenetic relationships of the large, diverse genus Apocephalus Coquillett are studied using seven loci (16S, COI, NDI, 28S, AK, CAD, and TPI). Both Bayesian and Maximum Likelihood methods were used to analyze the sequences. Pre-existing taxonomic relationships, based on morphology, were largely upheld, with the notable exception of the subgenus Mesophora Borgmeier being placed deep inside the genus. Therefore, Mesophora was synonymized with Apocephalus (new synonymy) and its species referred to as belonging to the Apocephalus wheeleri group. Both methods of analysis recovered similar results, providing what we consider reasonable explanations of the data, based on morphological information.

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Molecular phylogeny of common sun skink, Eutropis (Squamata: Scincidae), of northwestern part of Bangladesh

Bangladesh Journal of Zoology ◽

10.3329/bjz.v47i1.42017 ◽

2019 ◽

Vol 47 (1) ◽

pp. 13-25

Author(s):

Mosharrof Hossain ◽

Che Jing

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

16S Rrna ◽

Molecular Phylogeny ◽

Posterior Probability ◽

Common Ancestor ◽

Northwestern Part ◽

Congeneric Species ◽

Relationship Of ◽

Posterior Probability Support

A study on the phylogenetic relationship of Bangladeshi Skink confirmed species as Eutropis multifasciata by Bayesian inference (BI) (100%) and 98% node support to maximum likelihood (ML) tree topology, respectively. The sequence divergences between Eutropis multifasciata and other congeneric species were significant, ranging from 0.1 to 13.6% for 16S rRNA. Intraspecific genetic divergence within E. multifasciata was estimated 10.3%. E. multifasciata formed a distinct clade with high posterior probability support. This maiden study on Bangladeshi Skink results support that one monophyletic subgroup containing all specimens of E. multifasciata and all recently recognized E. multifasciata populations have evolved from one common ancestor. Bangladesh J. Zool. 47(1): 13-25, 2019

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Delving deeper into the phylogenetics of the herbaceous bamboos (Poaceae, Bambusoideae, Olyreae): evaluation of generic boundaries within the Parodiolyra/Raddiella clade uncovers a new genus

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz049 ◽

2019 ◽

Vol 192 (1) ◽

pp. 61-81 ◽

Cited By ~ 1

Author(s):

Iasmin L C Oliveira ◽

Andreza O Matos ◽

Christian Silva ◽

Maria Luiza S Carvalho ◽

Christopher D Tyrrell ◽

...

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Phylogenetic Relationships ◽

New Genus ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Morphological Evidence ◽

Taxon Sampling ◽

Plastid Genomes ◽

Herbaceous Bamboos

Abstract The present study aims to expand the knowledge of phylogenetic relationships in Olyrinae, a subtribe of herbaceous bamboos (Poaceae: Bambusoideae: Olyreae). Our focus is on Parodiolyra and Raddiella, two historically related genera that, with their sister Diandrolyra, form one of the four main lineages in the subtribe. Previous phylogenetic analyses suggested that Parodiolyra is not monophyletic, but its taxonomic boundaries and its relationship with Raddiella remain uncertain due to low sampling. We increased the taxon sampling and sequenced five regions of the nuclear and plastid genomes for this lineage and other representatives of Olyreae. We used maximum parsimony, maximum likelihood, Bayesian inference and coalescence analysis. Our results corroborate the paraphyly of Parodiolyra, with P. micrantha sister to a clade including the remaining Parodiolyra and Raddiella. All remaining Parodiolyra form a well-supported clade, but Raddiella had conflicting resolutions, being either monophyletic or not. Thus, based on phylogenetic and morphological evidence, we here recircumscribe Parodiolyra, transferring P. micrantha and P. colombiensis to the new genus Taquara (described here). Regarding Raddiella, sampling is still not comprehensive and does not allow a decision on to its taxonomic status to be made at this time. Inclusion of other phreatophytic species may be crucial to resolve the problem of conflicting topologies.

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A molecular phylogeny of Pilocarpaceae Zahlbr., including a new species of Tapellaria Müll. Arg. and new records of foliicolous lichenized fungi from Thailand

The Lichenologist ◽

10.1017/s0024282920000328 ◽

2020 ◽

Vol 52 (5) ◽

pp. 377-385

Author(s):

Wei-Cheng Wang ◽

Ek Sangvichien ◽

Tie-Zheng Wei ◽

Jiang-Chun Wei

Keyword(s):

New Species ◽

Maximum Likelihood ◽

Molecular Phylogeny ◽

Phylogenetic Relationships ◽

National Park ◽

New Records ◽

Lichenized Fungi ◽

Foliicolous Lichens ◽

Khao Yai National Park ◽

A New Species

AbstractThe phylogeny of foliicolous taxa in Pilocarpaceae was reconstructed using Bayesian and maximum likelihood analyses of concatenated ITS and mtSSU sequences. Sixty-six new partial sequences representing 36 taxa were generated and 29 sequences were downloaded from GenBank. Our results indicate that Lasioloma R. Sant. is nested within a paraphyletic Calopadia Vězda, whereas Fellhanera Vězda is polyphyletic and the phylogenetic relationships of Eugeniella Lücking et al. and Sporopodium Mont. with Fellhanera require further investigation. In addition, Tapellaria parvimuriformis W. C. Wang & J. C. Wei is described as a new species from Khao Yai National Park, Thailand, and is characterized by its small muriform ascospores, grey campylidia with a pale base, and short conidia. Eight new records of foliicolous lichens for Thailand are also listed.

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