Placing the forgotten: on the positions of Euenchytraeus and Chamaedrilus in an updated enchytraeid phylogeny (Clitellata : Enchytraeidae)

2017 ◽  
Vol 31 (1) ◽  
pp. 85 ◽  
Author(s):  
Svante Martinsson ◽  
Klára Dózsa-Farkas ◽  
Emilia Rota ◽  
Christer Erséus
Keyword(s):  
Maximum Likelihood ◽  
Bayes Factor ◽  
Nuclear Genes ◽  
Phylogenetic Study ◽  
Base Pairs ◽  
Anatomical Trait

The phylogeny of Enchytraeidae was re-estimated to establish the relationships of the now resurrected Chamaedrilus and Euenchytraeus and to confirm their status as separate taxa. The former Cognettia (Enchytraeidae) was recently revised and split into its two senior synonyms, Chamaedrilus and Euenchytraeus, with the majority of the species transferred to Chamaedrilus. Euenchytraeus was re-established for three species sharing a unique anatomical trait, but has never before been represented in any phylogenetic study. We included representatives from 21 (of 33) valid enchytraeid genera and used three mitochondrial and four nuclear genes. The dataset (4164 base pairs) was analysed using multi-species coalescent (MSC) and maximum likelihood (ML) methods. Chamaedrilus (represented by eight species) and Euenchytraeus (represented by Eu. clarae) were found in a clade together with the monotypic Stercutus. Chamaedrilus was found to be monophyletic with maximum support in both analyses. The ML tree supported Euenchytraeus and Chamaedrilus as sister groups, whereas the MSC tree placed Euenchytraeus together with Stercutus, both with low support. A Bayes factor test weakly supported Euenchytraeus and Chamaedrilus as sister groups over Euenchytraeus+Stercutus. Possible morphological synapomorphies for these genera are discussed, and we conclude that Chamaedrilus and Euenchytraeus are closely related, but their status as separate genera is justified.

A reassessment of apheloriine millipede phylogeny: additional taxa, Bayesian inference, and direct optimization (Polydesmida: Xystodesmidae)

Zootaxa ◽  
2007 ◽  
Vol 1610 (1) ◽  
pp. 27-39 ◽  
Author(s):  
PAUL E. MAREK ◽  
JASON E. BOND
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Bayes Factor ◽  
Appalachian Mountains ◽  
Deciduous Forests ◽  
Eastern United States ◽  
Undescribed Species ◽  
Direct Optimization ◽  
Species List ◽  
Phylogenetic Hypotheses

Millipedes in the tribe Apheloriini occur throughout the eastern United States, predominately in the deciduous forests of the Appalachian Mountains. Herein we present a reassessment of apheloriine millipede phylogeny using mitochondrial DNA sequences and an additional 29 exemplar taxa (including 15 undescribed species and all of the species in the genus Brachoria, except one). In this study, first we check the results of the previous phylogeny of the tribe (Marek and Bond, 2006) with different alignment and phylogenetic techniques (direct optimization and maximum likelihood), and second reconstruct a new phylogeny evaluating it in the same way with Bayesian, maximum likelihood, and direct optimization. Using this updated and expanded phylogeny, we tested historical classifications with Bayes factor and Shimodaira-Hasegawa hypothesis testing, consistently finding very strong evidence against their implied phylogenetic hypotheses. Lastly, using the new phylogeny as a foundation, we make taxonomic modifications and provide an updated species list of Apheloriini (106 species/17 genera).

scholarly journals A new species of the Dendropsophus parviceps group from the western Amazon Basin (Amphibia: Anura: Hylidae)

Zootaxa ◽  
2012 ◽  
Vol 3249 (1) ◽  
pp. 18 ◽  
Author(s):  
ANA P. MOTTA ◽  
SANTIAGO CASTROVIEJO-FISHER ◽  
PABLO J. VENEGAS ◽  
VICTOR G.D. ORRICO ◽  
JOSÉ M. PADIAL
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Amazon Basin ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Terra Firme ◽  
Base Pairs ◽  
White Spots ◽  
A New Species

We describe Dendropsophus frosti sp. nov. from lowland terra firme rainforests of the headwaters of the Amazon RiverBasin in Colombia and Peru. The new species is known from only two localities, the type locality near Leticia (Departa-mento Amazonas, Colombia, 04° 06' 24.2" S, 69° 56' 57.4" W; 103 m.a.s.l.), and the paratopotypic locality, Piedras in thePutumayo basin (Departamento Loreto, Peru, 02.79278° S, 72.91750° W; 90–170 m.a.s.l.). Maximum likelihood and par-simony analyses of 2436 aligned base pairs of the 12S and 16S rRNA genes recovered the new species as a member of D.parviceps group and sister to D. brevifrons. The new species is most closely related to D. parviceps, D. brevifrons, and D.koechlini, and it can be readily distinguished from these and all other members of the D. parviceps group by, among othercharacters, its plain dorsal light brown coloration, copper iris, plain immaculate pale yellow to white venter coloration, lack of flash marks on groin and axillae, and absence of white spots on lips.

scholarly journals Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu Sun ◽  
Hua Huang ◽  
Yudong Liu ◽  
Shanshan Liu ◽  
Jun Xia ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Rich Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Lepidopteran Insects

AbstractIn this study, we analyzed the complete mitochondrial genome (mitogenome) of Speiredonia retorta, which is a pest and a member of the Lepidoptera order. In total, the S. retorta mitogenome was found to contain 15,652 base pairs encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, as well as an adenine (A) + thymine (T)-rich region. These findings were consistent with the mitogenome composition of other lepidopterans, as we identified all 13 PCGs beginning at ATN codons. We also found that 11 PCGs terminated with canonical stop codons, whereas cox2 and nad4 exhibited incomplete termination codons. By analyzing the mitogenome of S. retorta using Bayesian inference (BI) and maximum likelihood (ML) models, we were able to further confirm that this species is a member of the Erebidae family.

A phylogenetic study of the Micarea prasina group shows that Micarea micrococca includes three distinct lineages

2009 ◽  
Vol 42 (1) ◽  
pp. 7-21 ◽  
Author(s):  
Paweł CZARNOTA ◽  
Beata GUZOW-KRZEMIŃSKA
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Small Subunit ◽  
Sister Species ◽  
Phylogenetic Study ◽  
Rdna Sequences ◽  
Small Subunit Ribosomal Dna

AbstractThe phylogeny of the Micarea prasina group was investigated using mitochondrial small subunit ribosomal DNA sequences from 14 taxa representing this group, four other members of the genus Micarea, and Psilolechia lucida as an outgroup. A total of 31 new mtSSU rDNA sequences were generated, including 10 from the M. micrococca complex. Bayesian, maximum parsimony (MP) and maximum likelihood (ML) methods were used to analyse the data. The results show that M. micrococca is not monophyletic and forms three strongly supported lineages: 1) M. micrococca s. str., 2) M. byssacea (Th. Fr.) Czarnota, Guzow-Krzemińska & Coppins comb. nov., and 3) a putative taxon that requires further studies. Micarea viridileprosa is a sister species to M. micrococca s. str. and the recently described M. nowakii is a sister species to M. prasina s. str. The placement of M. tomentosa within the M. prasina group is confirmed. Micarea hedlundii appears to be more closely related to the M. micrococca complex than M. prasina s. str. Descriptions, illustrations, taxonomic remarks, distribution and habitat data for M. micrococca s. str. and M. byssacea are provided. A lectotype for Biatora byssacea Hampe non Zwackh and a neotype for Catillaria prasina β [var.] byssacea are selected.

Phylogeny of Macronematinae (Trichoptera: Hydropsychidae) based on molecular and morphological analyses

2019 ◽  
Vol 151 (6) ◽  
pp. 696-716 ◽  
Author(s):  
Christine Jewel C. Uy ◽  
Ji Hyoun Kang ◽  
John C. Morse ◽  
Yeon Jae Bae
Keyword(s):  
Phylogenetic Relationships ◽  
Large Subunit ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Study ◽  
Base Pairs ◽  
Morphological Findings ◽  
Close Relationship ◽  
Evolutionary Novelties

AbstractThe phylogenetic relationships among the members of Macronematinae (Trichoptera: Hydropsychidae) have long been debated and often revised. Our study based on a large subunit (28S) nuclear ribosomal DNA (D2 expansion fragment; 464 base pairs) of gene sequences found all genera to be monophyletic except for the genus Polymorphanisus Walker, which produced two clades in accordance with its species groups established using morphological characters. Phylogenetic reconstruction based on mitochondrial cytochrome oxidase I (658 base pairs) found the same monophyletic relationships, however, except for the genera Polymorphanisus and Macrostemum Kolenati. The placement of the genus Leptonema Guérin-Méneville as the basal clade in the subfamily was also ruled out, which is consistent with previous morphological findings. The monophyly of two previously recognised tribes (Macronematini and Polymorphanisini) was not supported. We also found that the genera Centromacronema Ulmer, Baliomorpha Neboiss, and Macronema Pictet are most closely related, having three head setal warts on the vertex of the head and unsegmented inferior appendages of male genitalia as their synapomorphies. Our study supported the hypothesis of close relationship of the genera Amphipsyche McLachlan and Protomacronema Ulmer with the morphological synapomorphies: absence of a forewing discoidal cell and the presence of elevated head carinae on the larvae. Some notable evolutionary novelties in the structure of adults in various lineages of this subfamily include reduction of maxillae and labium, reduction and loss of a discoidal cell and evolution of a c-sc crossvein in each forewing, fusion of segments in each male inferior appendage, and evolution of dark colour patterns in the forewings. Also, the head setal warts, which are unique organs in Trichoptera, evolved towards a decreasing number in the subfamily. This first molecular phylogenetic study, covering most genera in Macronematinae and including an interpretation of 12 key evolutionary novelties, provides an important basis for resolving long-standing questions regarding phylogenetic relationships and classification of genera and species and helps lay a stronger foundation for inference of testable hypotheses about functional traits for species of this common and widespread subfamily.

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

Zootaxa ◽  
2019 ◽  
Vol 4565 (1) ◽  
pp. 108 ◽  
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. 

Phylogeny of the East Asian cyprinids inferred from sequences of the mitochondrial DNA control region

2003 ◽  
Vol 81 (12) ◽  
pp. 1938-1946 ◽  
Author(s):  
Huanzhang Liu ◽  
Yiyu Chen
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
East Asian ◽  
Molecular Data ◽  
Mtdna Control Region ◽  
Phylogenetic Study ◽  
Base Pairs ◽  
Fish Family ◽  
Representative Species ◽  
Morphological And Molecular Data

With 210 genera and 2010 species, Cyprinidae is the largest freshwater fish family in the world. Several papers, based on morphological and molecular data, have been published and have led to some solid conclusions, such as the close relationships between North American phoxinins and European leuciscins. However, the relationships among major subgroups of this family are still not well resolved, especially for those East Asian groups. In the present paper, the mitochondrial DNA (mtDNA) control region, 896–956 base pairs, of 17 representative species of East Asian cyprinids was sequenced and compared with those of 21 other cyprinids to study their phylogenetic relationships. After alignment, there were 1051 sites. The comparison between pairwise substitutions and HKY distances showed that the mtDNA control region was suitable for phylogenetic study. Phylogenetic analysis indicated that there are two principal lineages in Cyprinidae: Cyprinine and Leuciscine. In Cyprinine, the relationships could be a basal Labeoinae, an intermediate Cyprininae, and a diversified Barbinae (including Schizothroaxinae). In Leuciscine, Rasborinae is at the basal position; Gobioninae and Leuciscinae are sister groups; the East Asian cultrin–xenocyprinin taxa form a large mono phyl etic group with some small affiliated groups; and the positions of Acheilognathinae and Tincinae are still uncertain.

scholarly journals Phylogeography and ecology of an endemic radiation of Hawaiian aquatic case-bearing moths ( Hyposmocoma : Cosmopterigidae)

2008 ◽  
Vol 363 (1508) ◽  
pp. 3459-3465 ◽  
Author(s):  
Daniel Rubinoff
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Mitochondrial Gene ◽  
Hawaiian Islands ◽  
Elongation Factor ◽  
Nuclear Gene ◽  
Base Pairs ◽  
Island Endemic ◽  
Northwestern Hawaiian Islands ◽  
Elongation Factor 1

The endemic moth genus Hyposmocoma (Lepidoptera: Cosmopterigidae) may be one of the most speciose and ecologically diverse genera in Hawaii. Among this diversity is the Hyposmocoma saccophora clade with previously unrecorded aquatic larvae. I present a molecular phylogeny based on 773 base pairs (bp) of the mitochondrial gene cytochrome c oxidase subunit I and 762 bp of the nuclear gene elongation factor 1-α. Topologies were constructed from data using maximum-parsimony, maximum-likelihood and Bayesian search criteria. Results strongly support the monophyly of the H. saccophora clade and the monophyly of the genus Hyposmocoma . The H. saccophora clade has single-island endemic species on Oahu, Molokai and West Maui. By contrast, there are three species endemic to Kauai, two being sympatric. The H. saccophora clade appears to follow the progression rule, with more basal species on older islands, including the most basal species on 11 Myr-old Necker Island, one of the Northwestern Hawaiian Islands. Aquatic behaviour either evolved recently in the species on the main Hawaiian Islands or was secondarily lost on the arid northwestern Necker Island. The phylogeny suggests that Hyposmocoma is older than any of the current main islands, which may, in part, explain Hyposmocoma 's remarkable diversity.

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