A new species of  Polypedilum  ( Cerobregma ) ( Diptera ,  Chironomidae ) from Oriental China

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Abstract

Polypedilum ( Cerobregma) huapingensis Liu & Lin, sp. nov. is described and illustrated based on an adult male from Huaping National Nature Reserve, Guangxi, China. A DNA barcode analysis, including the known partial COI sequences of species in the Cerobregma subgenus, was conducted. An updated key to adult males of the subgenus Cerobregma is provided.

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Most cited references 29

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MUSCLE: multiple sequence alignment with high accuracy and high throughput.

R. C. Edgar (2004)

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

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MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Koichiro Tamura, Glen Stecher, Daniel Walter Peterson … (2013)

We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.

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Biological identifications through DNA barcodes.

Paul Hebert, Alina Cywinska, Shelley Ball … (2003)

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.

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Author and article information

Contributors

Wen-Bin Liu:

ORCID: https://orcid.org/0000-0001-6916-0692

Xiao-Long Lin:

ORCID: https://orcid.org/0000-0001-6544-6204

Journal

Journal ID (nlm-ta): Zookeys

Journal ID (iso-abbrev): Zookeys

Journal ID (publisher-id): 2

Journal ID (index): urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E

Journal ID (aggregator): urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A

Title: ZooKeys

Publisher: Pensoft Publishers

ISSN (Print): 1313-2989

ISSN (Electronic): 1313-2970

Publication date Collection: 2021

Publication date (Electronic): 22 January 2021

Volume: 1011

Pages: 139-148

Affiliations

[1 ] Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, 300387, China Tianjin Normal University Tianjin China

[2 ] College of Life Sciences, Nankai University, Tianjin, 300071, China Nankai University Tianjin China

Author notes

Corresponding author: Xiao-Long Lin ( lin880224@ 123456gmail.com )

Academic editor: F.L. da Silva

Author information

Wen-Bin Liu https://orcid.org/0000-0001-6916-0692

Xiao-Long Lin https://orcid.org/0000-0001-6544-6204

Article

Publisher ID: 59554

DOI: 10.3897/zookeys.1011.59554

PMC ID: 7847467

PubMed ID: 33568962

SO-VID: fa7bde59-e1a1-4f1e-aae6-226350d0fd96

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 11 October 2020

Date accepted : 15 December 2020

Funding

Financial support from National Natural Science Foundation of China (31672264, 31672324, 31801994, 31900344), the China Postdoctoral Science Foundation Grant (2018M640227), GDAS Special Project of Science and Technology Development (No. 2020GDASYL-20200102021, 2020GDASYL-20200301003) and Natural Science Foundation of Tianjin (18JCQNJC14700, 18JCYBJC96100) are acknowledged with thanks.

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A new species of Polypedilum ( Cerobregma) (Diptera, Chironomidae) from Oriental China

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Abstract

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Pensoft Biodiversity

Most cited references 29

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Biological identifications through DNA barcodes.

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