Description of a new species of glass knifefish genus Eigenmannia (Gymnotiformes: Sternopygidae) from the upper rio Paraná basin, based on anatomical, karyotypic, and molecular evidences

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Abstract

Abstract A new species of Eigenmannia is described from the upper rio Paraná basin based on morphological and molecular data. It is distinguished for all congeners by a unique combination of morphometrics, meristics, osteological characters, a significant COI genetic divergence that ranges from 4.9 to 15.2%, and its karyotype. An osteological description for the new species is provided, the geographic distribution of Eigenmannia species in the upper rio Paraná basin is commented on, and the use of karyotype information in taxonomic studies is discussed.

Translated abstract

Resumo Uma espécie nova de Eigenmannia é descrita da bacia do alto rio Paraná, com base em dados morfológicos e moleculares. Distingue-se de todas as congêneres por uma combinação única de caracteres morfométricos, merísticos, osteológicos, uma significativa divergência genética que varia de 4,9 a 15,2%, e pelo seu cariótipo. Uma descrição osteológica para a nova espécie é fornecida, a distribuição geográfica das espécies de Eigenmannia na bacia do alto rio Paraná é comentada, e o uso da informação do cariótipo em estudos taxonômicos é discutido.

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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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MEGA11: Molecular Evolutionary Genetics Analysis Version 11

Koichiro Tamura, Glen Stecher, Sudhir Kumar (2021)

The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor , and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net .

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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

Motoo Kimura (1980)

Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.

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Journal

Journal ID (publisher-id): ni

Title: Neotropical Ichthyology

Abbreviated Title: Neotrop. ichthyol.

Publisher: Sociedade Brasileira de Ictiologia (Maringá, PR, Brazil )

ISSN (Print): 1679-6225

ISSN (Electronic): 1982-0224

Publication date (Print and electronic): 2023

Volume: 21

Issue: 4

Electronic Location Identifier: e230090

Affiliations

[3] Passos MG orgnameUniversidade do Estado de Minas Gerais, Unidade Acadêmica Passos Brazil guilhermedutr@ 123456yahoo.com.br

[1] São Paulo São Paulo orgnameUniversidade de São Paulo orgdiv1Programa de Pós-Graduação em Zoologia orgdiv2Instituto de Biociências Brazil viniciusc.cardoso@ 123456yahoo.com.br

[2] São Paulo São Paulo orgnameUniversidade de São Paulo orgdiv1Museu de Zoologia Brazil

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Publisher ID: S1679-62252023000400205 Publisher ID: S1679-6225(23)02100400205

DOI: 10.1590/1982-0224-2023-0090

SO-VID: 3d92a9b7-ffd4-4ed1-a4e8-327a29d7b991

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This work is licensed under a Creative Commons Attribution 4.0 International License.

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Date accepted : 11 October 2023

Date received : 03 August 2023

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Figures: 0, Tables: 0, Equations: 0, References: 56, Pages: 0

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Description of a new species of glass knifefish genus Eigenmannia (Gymnotiformes: Sternopygidae) from the upper rio Paraná basin, based on anatomical, karyotypic, and molecular evidences

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SciELO Brazil

Most cited references 55

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

MEGA11: Molecular Evolutionary Genetics Analysis Version 11

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

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