Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence

Larval black flies, especially earlier instars, can be difficult to associate morphologically and chromosomally with other life stages. We used sequences of mitochondrial cytochrome c oxidase I (COI) and nuclear elongation complex protein 1 (ECP1) to associate unknown larvae with known species of the Simulium multistriatum species group in Thailand. COI barcode sequences failed to differentiate closely related species (S. chaliowae, S. lampangense, and S. fenestratum) and unknown larvae. In contrast, ECP1 sequences clearly separated these species, and revealed that the unknown larvae clustered with pupae of S. lampangense. The larva of S. lampangense is described morphologically for the first time. It is similar to that of S. chaliowae, but can be distinguished by a pair of dorsal protuberances on segments 3–7 rather than on segments 2–6.

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A phylogeny for side-necked turtles (Chelonia: Pleurodira) based on mitochondrial and nuclear gene sequence variation

Biological Journal of the Linnean Society ◽

10.1111/j.1095-8312.1999.tb01862.x ◽

1999 ◽

Vol 67 (2) ◽

pp. 213-246 ◽

Cited By ~ 65

Author(s):

A. GEORGES ◽

J. BIRRELL ◽

K. M. SAINT ◽

W. McCORD ◽

S. C. DONNELLAN

Keyword(s):

Sequence Variation ◽

Gene Sequence ◽

Nuclear Gene ◽

Nuclear Gene Sequence

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The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0034 ◽

2009 ◽

Vol 364 (1527) ◽

pp. 2197-2207 ◽

Cited By ~ 82

Author(s):

Peter G. Foster ◽

Cymon J. Cox ◽

T. Martin Embley

Keyword(s):

Sequence Data ◽

Phylogenetic Signal ◽

Amino Acid Sequences ◽

Rate Variation ◽

Molecular Sequence Data ◽

Protein Coding ◽

Molecular Sequence ◽

Heterogeneous Models ◽

Matrix Heterogeneity ◽

Rna Genes

The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the ‘eocyte hypothesis’, where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.

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Gene Sequence Analysis of Mitochondrial COI in Genus Saperda (Coleoptera: Cerambycidae: Lamiinae)

10.3897/arphapreprints.e70782 ◽

2021 ◽

Author(s):

Wei XU ◽

Qinhua Gan ◽

Jian Pu ◽

Yingwen Pan ◽

Bo Cai ◽

...

Keyword(s):

Sequence Analysis ◽

Detection Rate ◽

Gene Sequence ◽

Mitochondrial Gene ◽

Dna Barcode ◽

Nuclear Gene ◽

Rapid Identification ◽

Mitochondrial Coi ◽

Gene Sequence Analysis ◽

Total Dna

In this study, the total DNA of nine species of Saperda (Lopezcolonia) octopunctata (Scopoli, 1772), Saperda (Lopezcolonia) scalaris (Linnaeus, 1758), Saperda interrupta Gebler, Saperda Alberti (Plavilstshikov), Saperda (Saperda) similis Laicharting, 1784, Saperda (Compsidia) populnea (Linnaeus, 1758), Saperda (Saperda) carcharias (Linnaeus, 1758), Saperda (Lopezcolonia) perforata Pallas, 1773 and Saperda ohbayashi were extracted. Two partial sequences of mitochondrial gene and one partial sequence of nuclear gene were amplified. Comparing the COI sequence with the DNA barcode data in GenBank can effectively identify the related species of Saperda. It will be applied to the rapid identification of some species of Saperda in imported wood at ports, and improve the detection rate of plant quarantine.

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Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

Systematic Botany ◽

10.1600/036364421x16128061189576 ◽

2021 ◽

Vol 46 (1) ◽

pp. 162-174

Author(s):

Ming-Hui Yan ◽

Chun-Yang Li ◽

Peter W. Fritsch ◽

Jie Cai ◽

Heng-Chang Wang

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Signal ◽

Strong Support ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

The Family ◽

Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

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The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism

Parasitology ◽

10.1017/s0031182011001089 ◽

2011 ◽

Vol 138 (13) ◽

pp. 1760-1777 ◽

Cited By ~ 30

Author(s):

LAURA M. McDONAGH ◽

JAMIE R. STEVENS

Keyword(s):

Sequence Data ◽

Single Gene ◽

Nuclear Gene ◽

Evolutionary Status ◽

28S Rrna ◽

Gene Trees ◽

Data Set ◽

Protein Coding ◽

Nucleotide Sequence Data ◽

The Family

SUMMARYThe Calliphoridae include some of the most economically significant myiasis-causing flies in the world – blowflies and screwworm flies – with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.

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The Molecular Phylogeny of the New Zealand Endemic Genus Hadramphus and the Revival of the Genus Karocolens

Diversity ◽

10.3390/d10030088 ◽

2018 ◽

Vol 10 (3) ◽

pp. 88

Author(s):

Emily Fountain ◽

Robert Cruickshank ◽

Adrian Paterson

Keyword(s):

New Zealand ◽

Gene Sequence ◽

Mitochondrial Gene ◽

Single Gene ◽

Morphological Characteristics ◽

Nuclear Gene ◽

Similar Species ◽

Morphological Similarity ◽

Coalescent Approach ◽

Systematic Relationships

The delineation of species is important to the fields of evolution, ecology and conservation. The use of only a single line of evidence, e.g., morphology or a single gene sequence, may underestimate or overestimate the level of diversity within a taxon. This problem often occurs when organisms are morphologically similar but genetically different, i.e., for cryptic species. The Hadramphus genus contains four endangered, morphologically similar species of weevils, each endemic to a specific New Zealand region (Hadramphus spinipennis Chatham Islands, H. stilbocarpae Fiordland, H. tuberculatus McKenzie Country, H. pittospori Poor Knights Islands). The systematic relationships among these species are unclear. We used samples from these species and a closely related genus, Lyperobius huttoni, to obtain data from the mitochondrial gene cytochrome c oxidase subunit I and the nuclear gene internal transcribe spacer 2. In addition to the multi-locus coalescent approach, we modelled morphological characteristics combined with the genetic data. We found that H. spinipennis, H. tuberculatus and H. stilbocarpae were a closely related clade. Despite a strong morphological similarity, Hadramphus pittospori was found to be genetically distinct from the other Hadramphus species, which supports the resurrection of the monotypic genus Karocolens for this species.

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