scholarly journals Phylogenetics of a small caddisfly genus (Thremmatidae: Oligophlebodes): comparison among multiple hypotheses from DNA barcode data

Zoosymposia ◽  
2019 ◽  
Vol 14 (1) ◽  
pp. 193-203
Author(s):  
DANA WEAVER ◽  
JOSEPH C. SPAGNA ◽  
PATINA K. MENDEZ
Keyword(s):  
Single Gene ◽  
Dna Barcode ◽  
Coi Gene ◽  
The Novel ◽  
Gene Trees ◽  
Likelihood Methods ◽  
Basal Node ◽  
Distance Methods ◽  
Likelihood Analysis ◽  
Codon Positions

Barcoding datasets can serve as a resource for species associations and delineations, but single-gene trees estimated by distance methods do not provide strong estimates of phylogeny. Using DNA data from the Barcode of Life Database (BOLD), we calculate a phylogenetic tree for Oligophlebodes (Trichoptera: Thremmatidae), a small genus of caddisfly endemic to the Western United States. Here we estimate a preliminary phylogeny for Oligophlebodes using Bayesian likelihood, and compare it to trees produced by distance and standard likelihood methods. Using the barcode region of the cytochrome oxidase 1 (COI) gene, we analyzed 44 individuals representing five species (and 2 unknowns) and a sister-genus outgroup (Neophylax) from locations ranging from Southern New Mexico northwest into British Columbia. Partitioned Bayesian likelihood analysis under the F81 (1st codon positions) and HKY80 + I + Γ (for both the 2nd and 3rd codon positions) model gave the consensus topology (Neophylax toshi, (O. sierra, (O. ruthae inc. spc. 1 & 2, O. sigma, (spc. 3 & 4, (O. ardis, O. minutus)))). Species identifications were supported by monophyly of most species-level taxa. However, confirmation of species identifications of unknowns was complicated by incomplete taxon sampling for spc. 1 & 2. Placement of spc. 3 & 4 may serve as support for taxonomic review of O. minutus. Compared with an existing published phylogeny of Oligophlebodes BOLD sequences constructed under RAxML, the Bayesian hypothesis had higher resolution at the basal node of Oligophlebodes. Because of their support values, both likelihood trees are recommended over the BOLD TaxonID tree (an unrooted neighbor joining tree using the Kimura 2-parameter model). The novel topology produced in the Bayesian tree supports further explorations by likelihood-based methods, including partitioned analyses, of our preliminary Oligophlebodes dataset that can be used as additional lines of evidence to support morphological work.

scholarly journals Monophyly of Diverse Bigyromonadea and their Impact on Phylogenomic Relationships Within Stramenopiles

2021 ◽  
Author(s):  
Anna Cho ◽  
Denis V. Tikhonenkov ◽  
Elisabeth Hehenberger ◽  
Anna Karnkowska ◽  
Patrick J. Keeling
Keyword(s):  
Maximum Likelihood ◽  
Single Gene ◽  
The Novel ◽  
Gene Trees ◽  
Genomic Information ◽  
Bayesian Analyses ◽  
And Topology ◽  
First Case ◽  
Topology Testing ◽  
Eukaryotic Supergroup

Stramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of the group. This is most obvious in Bigyromonadea, which is one of four major stramenopile subgroups but represented by a single transcriptome. To examine the diversity of Bigyromonadea and how the lack of data affects the tree, we generated transcriptomes from seven novel bigyromonada species described in this study: Develocauda condao, Develocanicus komovi, Develocanicus vyazemskyi, Cubaremonas variflagellatum, Pirsonia chemainus, Feodosia pseudopoda, and Koktebelia satura. Both maximum likelihood and Bayesian phylogenomic trees based on a 247 gene-matrix recovered a monophyletic Bigyromonadea that includes two diverse subgroups, Developea and Pirsoniales, that were not previously related based on single gene trees. Maximum likelihood analyses show Bigyromonadea related to oomycetes, whereas Bayesian analyses and topology testing were inconclusive. We observed similarities between the novel bigyromonad species and motile zoospores of oomycetes in morphology and the ability to self-aggregate. Rare formation of pseudopods and fused cells were also observed, traits that are also found in members of labyrinthulomycetes, another osmotrophic stramenopiles. Furthermore, we report the first case of eukaryovory in the flagellated stages of Pirsoniales. These analyses reveal new diversity of Bigyromonadea, and altogether suggest their monophyly with oomycetes, collectively known as Pseudofungi, is the most likely topology of the stramenopile tree.

scholarly journals Molecular and Morphological Assessment of Septoria Species Associated with Ornamental Plants in Yunnan Province, China

2021 ◽  
Vol 7 (6) ◽  
pp. 483
Author(s):  
Yuan-Yan An ◽  
Monika C. Dayarathne ◽  
Xiang-Yu Zeng ◽  
Alan J. L. Phillips ◽  
Kevin D. Hyde ◽  
...  
Keyword(s):  
Yunnan Province ◽  
Species Recognition ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Ornamental Plants ◽  
Dna Barcode ◽  
Botanical Garden ◽  
Rapid Identification ◽  
Gene Trees ◽  
Genealogical Concordance

The Karst landform is the main geographic characteristic in South China. Such areas are rich in vegetation and especially suitable for growth of shrubs and herbaceous plants. In this study, 11 Septoria strains were obtained from different plants’ leaves collected in the Kunming Botanical Garden, Yunnan Province, China. Based on single-gene and multi-gene analyses of five gene loci (tef1, rpb2, tub2, ITS, and LSU) and four gene regions (without LSU), these strains were found to belong to three independent phylogenetic lineages representing five species, including four novel taxa, and one new record for China. Five single gene trees were also provided to evaluate the effectiveness of each gene for discriminating the species, as a result of which tub2 was found to have the most suitable DNA barcode for rapid identification. Morphological descriptions, illustrations, and comparisons are provided for a more comprehensive assessment. Genealogical Concordance Phylogenetic Species Recognition (GCPSR) with a pairwise homoplasy index (PHI) test was used to evaluate the conclusions of the phylogenetic analyses.

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

A new species of the genus Parapentacentrus Shiraki, 1930 from Yunnan, China (Orthoptera: Gryllidae: Itarinae)

Zootaxa ◽  
2021 ◽  
Vol 5032 (1) ◽  
pp. 143-146
Author(s):  
YI-JIAO LIU ◽  
ZHU-QING HE
Keyword(s):  
New Species ◽  
Male Genitalia ◽  
Dna Barcode ◽  
Coi Gene ◽  
East China ◽  
Anal Plate ◽  
Type Specimens ◽  
Normal University ◽  
One New Species ◽  
A New Species

The genus Parapentacentrus Shiraki, 1930 includes two species with long wings. In this paper, we report one new species, P. brevipennis He sp. nov., from Jinping, Yunnan, China. The new species have short forewings and hindwings, and have differences in the shape of supra-anal plate and male genitalia. DNA Barcode (COI gene) of this new species are provided. The type specimens are deposited in Museum of Biology, East China Normal University (ECNU).  

No longer endemic to Africa: Kribiodosis Kieffer, 1921 (Diptera, Chironomidae) new to Oriental China with a phylogeny and expanded adult generic diagnoses

Zootaxa ◽  
2021 ◽  
Vol 5072 (6) ◽  
pp. 560-574
Author(s):  
WU HAN ◽  
JIE LIU ◽  
YIFAN LUO ◽  
HONGQU TANG
Keyword(s):  
New Species ◽  
Mixed Model ◽  
Dna Barcode ◽  
Sister Group ◽  
Phylogenetic Position ◽  
Generic Diagnosis ◽  
Likelihood Methods ◽  
Core Member ◽  
Maximum Likelihood Methods ◽  
African Genus

Kribiodosis Kieffer, 1921, an African genus of Chironomini (Diptera: Chironomidae), is newly recorded from the Oriental region through a new species K. cantonensis sp. n. Detailed descriptions of the male, female and a DNA barcode are provided. With the inclusion of the new species bearing scutal tubercle and fused tibial comb, the generic diagnosis needs revision and expansion. The phylogenetic position of Kribiodosis within the tribe Chironomini is explored based on five concatenated genetic makers (18S, 28S, CAD1, CAD4 and COI-3P) using both mixed-model Bayesian inference and maximum likelihood methods. Kribiodosis is placed as a core member of the Microtendipes group but its precise sister group remains unclear. Inclusion of the analysis of Nilodosis Kieffer, another Chironomini genus with an African-Oriental distribution, reveals an unexpected robust position as sister to a large and diverse inclusive group of many Chironomini.  

scholarly journals Genetic Diversity and Population Structure of Metaphire vulgaris Based on the Mitochondrial COI Gene and Microsatellites

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Fang ◽  
Jie Chen ◽  
Honghua Ruan ◽  
Nan Xu ◽  
Ziting Que ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coi Gene ◽  
Small Scale ◽  
The Novel ◽  
Mitochondrial Coi ◽  
Allele Number ◽  
Medicinal Value ◽  
Mitochondrial Coi Gene ◽  
Data Content ◽  
Genetic Structures

The earthworm species Metaphire vulgaris (a member of the Clitellata class) is widely distributed across China, and has important ecological functions and medicinal value. However, investigations into its genetic diversity and differentiation are scarce. Consequently, we evaluated the genetic diversity of five populations of M. vulgaris (GM, HD, NYYZ, QDDY, and QDY) in Yancheng, China via the mitochondrial COI gene and the novel microsatellites developed there. A total of nine haplotypes were obtained by sequencing the mitochondrial COI gene, among which NYYZ and QDDY populations had the greatest number of haplotypes (nh = 5). Further, the nucleotide diversity ranged from 0.00437 to 0.1243. The neighbor-joining trees and the TCS network of haplotypes indicated that earthworm populations within close geographical range were not genetically isolated at these small scale distances. Results of the identification of microsatellite molecular markers revealed that the allele number in 12 microsatellite loci ranged from 4 to 13. The observed heterozygosity ranged from 0.151 to 0.644, whereas the expected heterozygosity ranged from 0.213 to 0.847. The polymorphism data content of most sites was >0.5, which indicated that the designed sites had high polymorphism. Structural analysis results indicated that GM, HD, and NYYZ had similar genetic structures across the five populations. The Nei’s genetic distance between HD and NYYZ populations was the smallest (Ds = 0.0624), whereas that between HD and QDY populations was the largest (Ds = 0.2364). The UPGMA tree showed that HD were initially grouped with NYYZ, followed by GM, and then with QDDY. Furthermore, cross-species amplification tests were conducted for Metaphire guillelmi, which indicated that the presented markers were usable for this species. This study comprised a preliminary study on the genetic diversity of M. vulgaris, which provides basic data for future investigations into this species.

A multiplex PCR method for identification of two common true cutworm species (Lepidoptera: Noctuidae) tested in the central plain of Guilan province, Iran

Zootaxa ◽  
2018 ◽  
Vol 4420 (2) ◽  
pp. 243
Author(s):  
REZA HOSSEINI ◽  
KHADIJEH MADAHI
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Coi Gene ◽  
Molecular Diagnostic ◽  
Pest Species ◽  
Immature Stages ◽  
Nucleotide Polymorphisms ◽  
Peridroma Saucia ◽  
Lepidoptera Noctuidae ◽  
Guilan Province

Many species of cutworms (Lepidoptera: Noctuidae) are important agricultural pest. They feed on roots and foliage of their host plants. Traditionally these species are identified based on morphological characteristics of adults. Hence identification of specimens in poor condition, immature stages and also closely related species or cryptic species is a difficult task. The basics of biological and ecological studies largely rely on an accurate species identification; consequently these investigations are impacted by potential misidentifications. In this study, we amplified 5' region of mitochondrial c cytochrome oxidase subunit I (COI) gene (DNA barcode region) of various common true cutworm species including Agrotis ipsilon (Hufnagel, 1766), Agrotis exclamationis (Linnaeus, 1758), Peridroma saucia (Hübner, 1808) and Xestia c-nigrum (Linnaeus, 1758) from agricultural fields of Guilan province (North of Iran). We were able to detect 66 conservative Single Nucleotide Polymorphisms (SNPs) among the targeted pest species and eventually design specific primers and develop a multiplex polymerase chain reaction assay as a molecular diagnostic tool for immature stages of two the most common and abundant species including A. ipsilon and X. c-nigrum in Guilan province. 

Revision of the nearctic blister beetle genus Tricrania LeConte, 1860 (Coleoptera: Meloidae: Nemognathinae)

Zootaxa ◽  
2011 ◽  
Vol 2832 (1) ◽  
pp. 1 ◽  
Author(s):  
ANDREW R. CLINE ◽  
JEFFREY P. HUETHER
Keyword(s):  
Dna Barcode ◽  
Coi Gene ◽  
Additional Source ◽  
Taxonomic History ◽  
History Of ◽  
Species Descriptions ◽  
New Synonymy ◽  
Mitochondrial Cytochrome Oxidase ◽  
Blister Beetle ◽  
Distributional Limits

Tricrania LeConte is revised. One new synonymy is proposed: T. murrayi LeConte 1860 = T. stansburii (Haldeman) 1852, syn. nov. More than 1000 specimens of T. sanguinipennis (Say) and over 1100 specimens of T. stansburii were assessed to provide accurate host data, phenological periods, and distributional limits for each species. Descriptions of adults and 1 st instar larvae, diagnostic characters, and identification keys also are provided. A 565-bp fragment of mtDNA from the mitochondrial cytochrome oxidase 1 (COI) gene, i.e. the DNA barcode region, is provided as an additional source for identification. A taxonomic history of the genus and inclusive species is given, as well as remarks on the placement of Tricrania in Nemognathinae.

scholarly journals Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

2020 ◽  
Author(s):  
Matthew H Van Dam ◽  
James B Henderson ◽  
Lauren Esposito ◽  
Michelle Trautwein
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Gene Tree ◽  
Single Copy ◽  
Species Tree ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Reconstruction

Abstract Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

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