scholarly journals Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda)

Genome ◽  
2017 ◽  
Vol 60 (2) ◽  
pp. 169-182 ◽  
Author(s):  
Robert G. Young ◽  
Cathryn L. Abbott ◽  
Thomas W. Therriault ◽  
Sarah J. Adamowicz
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Graphical Method ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Threshold Value ◽  
Quantitative Comparison ◽  
Data Set ◽  
Pairwise Sequence Divergence ◽  
Marine Realm

DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value. With these thresholds, and using a newly generated planktonic marine data set, we quantify the degree of concordance using a bidirectional analysis and discuss different analytical methods for sequence-based species delimitation (e.g., BIN, ABGD, jMOTU, UPARSE, Mothur, PTP, and GMYC). Our results support a COI-5P threshold between 2.1% and 2.6% p-distance across methods for these crustacean taxa, yielding molecular groupings largely concordant with traditional, morphologically defined species. The adoption of internal methods for clustering verification enables rapid biodiversity studies and the exploration of unknown faunas using DNA barcoding. The approaches taken here for concordance assessment also provide a more quantitative comparison of clustering results (as contrasted with “success/failure” of barcoding), and we recommend their further consideration for barcoding studies.

scholarly journals Excluding spatial sampling bias does not eliminate over-splitting in DNA-based species delimitation analyses

2021 ◽  
Author(s):  
Daniel Lukic ◽  
Jonas Eberle ◽  
Jana Thormann ◽  
Carolus Holzschuh ◽  
Dirk Ahrens
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Incomplete Lineage Sorting ◽  
Sampling Bias ◽  
Lineage Sorting ◽  
Data Set ◽  
Dna Taxonomy ◽  
Operational Taxonomic Units ◽  
And Performance ◽  
Single Locality

DNA-barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affect the accuracy and performance of DNA-barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical data set sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivore chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analysed for a total of 186 individuals of 56 morphospecies. Tree based and distance based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. PTP and TCS prevailingly over-splitted morphospecies, while 3% clustering and ABGD also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs were discussed in the context of historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.

scholarly journals DNA Barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae)

Zootaxa ◽  
2007 ◽  
Vol 1423 (1) ◽  
pp. 1-26 ◽  
Author(s):  
JEFFREY H. SKEVINGTON ◽  
CHRISTIAN KEHLMAIER ◽  
GUNILLA STÅHLS
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Base Pairs ◽  
Data Set ◽  
Taxonomic Decision ◽  
Morphological Species

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

scholarly journals Challenging species delimitation in Collembola: cryptic diversity among common springtails unveiled by DNA barcoding

2012 ◽  
Vol 26 (6) ◽  
pp. 470 ◽  
Author(s):  
D. Porco ◽  
A. Bedos ◽  
Penelope Greenslade ◽  
C. Janion ◽  
D. Skarżyński ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Functional Groups ◽  
Species Delimitation ◽  
Sequence Divergence ◽  
Cryptic Diversity ◽  
Congeneric Species ◽  
Nuclear Marker ◽  
Accurate Identification ◽  
Intraspecific Divergence

Collembola is one of the major functional groups in soil as well as a model taxon in numerous disciplines. Therefore the accurate identification of specimens is critical, but could be jeopardised by cases of cryptic diversity. Several populations of six well characterised species of springtails were sequenced using the COI barcode fragment as a contribution to the global Collembola barcoding campaign. Each species showed high intraspecific divergence, comparable to interspecific sequence divergence values observed in previous studies and in 10 congeneric species barcoded here as a reference. The nuclear marker, 28S, confirmed all the intraspecific lineages found with COI, supporting the potential specific status of these entities. The implications of this finding for taxonomy and for disciplines relying on species names, such as evolution and ecology, are discussed.

scholarly journals Phylogenetic Relationships of Micronesian White-Eyes Based on Mitochondrial Sequence Data

The Auk ◽  
2000 ◽  
Vol 117 (2) ◽  
pp. 355-365 ◽  
Author(s):  
Beth Slikas ◽  
Isaac B. Jones ◽  
Scott R. Derrickson ◽  
Robert C. Fleischer
Keyword(s):  
Genetic Divergence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Single Species ◽  
Additional Species ◽  
Data Set ◽  
Mitochondrial Sequence ◽  
Sister Relationships ◽  
Optimal Trees

Abstract Using mitochondrial sequence data, we estimated phylogenetic relationships and genetic divergence among selected species of white-eyes (Zosteropidae). We focused on taxa endemic to islands in Micronesia, specifically Zosterops conspicillatus, Z. semperi, Z. hypolais, Rukia oleaginea, and Cleptornis marchei. We also included in our data set five additional species of Zosterops from the Indo-Australian region and three species from Africa, as well as additional passerine outgroups. Our mitochondrial sequence data revealed substantial genetic divergence (5.7 to 7.3%) among Z. conspicillatus, Z. semperi, and Z. hypolais, three taxa that formerly were treated as a single species. In addition, a sequence divergence of 6.5 ± SE of 1.7% was found between the population of Z. conspicillatus from Rota and “conspecific” populations on Guam, Tinian, and Saipan. The distinctiveness of the Rota population suggests that this taxon should be recognized as a distinct species, a result that bears on the conservation of this population because it has been declining dramatically in recent years. All optimal trees based on analysis of the mitochondrial sequence data place Rukia oleaginea within the genus Zosterops. In all optimal trees, Cleptornis marchei positions as the sister taxon to a clade including all other zosteropids included in this study. The trees based on our data strongly contradict the traditional classification of Cleptornis as a honeyeater (family Meliphagidae). Our data cannot resolve with any confidence the sister relationships of the insular endemic white-eyes, although the optimal trees suggest multiple colonizations of Micronesia by more than one white-eye lineage.

scholarly journals The art and science of species delimitation

2015 ◽  
Vol 61 (5) ◽  
pp. 846-853 ◽  
Author(s):  
Bruce Rannala
Keyword(s):  
Full Advantage ◽  
Dna Barcoding ◽  
Bayesian Methods ◽  
Species Delimitation ◽  
Sequence Data ◽  
Art And Science ◽  
Approximate Methods ◽  
Sequencing Technologies ◽  
Identification Of Species ◽  
Half Decade

Abstract DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the framework of the multi-species coalescent (MSC). In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation (and their limitations) are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today’s technologies.

scholarly journals DNA Barcoding of Penaeidae (Decapoda; Crustacea): Non-Distance-Based Species Delimitation of the Most Economically Important Shrimp Family

Diversity ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 460
Author(s):  
Jorge L. Ramirez ◽  
Luisa Simbine ◽  
Carla G. Marques ◽  
Eliana Zelada-Mázmela ◽  
Lorenzo E. Reyes-Flores ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Mitochondrial Gene ◽  
Single Gene ◽  
Penaeid Shrimp ◽  
Genetic Distances ◽  
Structured Populations ◽  
Nominal Species ◽  
Data Set ◽  
Shrimp Fishery

The Penaeidae family includes some of the most economic and ecological important marine shrimp, comprising hundreds of species. Despite this importance and diversity, the taxonomic classification for penaeid shrimp has constantly been revised, and issues related to the species identification are common. In this study, we implemented DNA barcoding analyses in addition to single-gene species delimitation analyses in order to identify molecular operational taxonomy units (MOTUs) and to generate robust molecular information for penaeid shrimp based on the cytochrome oxidase subunit I (COI) mitochondrial gene. Our final data set includes COI sequences from 112 taxa distributed in 23 genera of penaeids. We employed the general mixed Yule coalescent (GMYC) model, the Poisson tree processes (PTP), and the Bayesian PTP model (bPTP) for MOTUs delimitation. Intraspecific and interspecific genetic distances were also calculated. Our findings evidenced a high level of hidden diversity, showing 143 MOTUs, with 27 nominal species not agreeing with the genetic delimitation obtained here. These data represent potential new species or highly structured populations, showing the importance of including a non-distance-based species delimitation approach in biodiversity studies. The results raised by this study shed light on the Penaeidae biodiversity, addressing important issues about taxonomy and mislabeling in databases and contributing to a better comprehension of the group, which can certainly help management policies for shrimp fishery activity in addition to conservation programs.

scholarly journals DNA barcoding of Zygaenidae (Lepidoptera): results and perspectives

2019 ◽  
Vol 42 (2) ◽  
pp. 137-150
Author(s):  
Konstantin A. Efetov ◽  
Anna V. Kirsanova ◽  
Zoya S. Lazareva ◽  
Ekaterina V. Parshkova ◽  
Gerhard M. Tarmann ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Coi Gene ◽  
Dna Barcodes ◽  
The Family ◽  
The World ◽  
Biological Characters

The present study provides a DNA barcode library for the world Zygaenidae (Lepidoptera). This study reports 1031 sequence data of the COI gene DNA barcodes for more than 240 species in four of the five subfamilies of the family Zygaenidae. This is about 20% of the world Zygaenidae species. Our results demonstrate the specificity of the COI gene sequences at the species level in most of the studied Zygaenidae and agree with already established taxonomic opinions. The study confirms the effectiveness of DNA barcoding as a tool for determination of most Zygaenidae species. However, some of the results are contradictory. Some cases of shared barcodes have been found, as well as cases of deep intraspecific sequence divergence in species that are well separated by morphological and biological characters. These cases are discussed in detail. Overall, when combined with morphological and biochemical data, as well as biological and ecological observations, DNA barcoding results can be a useful support for taxonomic decisions.

scholarly journals Six new Cyrtodactylus (Squamata: Gekkonidae) from northeast India

Zootaxa ◽  
2018 ◽  
Vol 4524 (5) ◽  
pp. 501 ◽  
Author(s):  
ISHAN AGARWAL ◽  
STEPHEN MAHONY ◽  
VARAD B. GIRI ◽  
R. CHAITANYA ◽  
AARON M. BAUER
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Northeast India ◽  
Morphological Data ◽  
Colour Pattern ◽  
Mitochondrial Sequence ◽  
Pairwise Sequence Divergence ◽  
Indian City ◽  
Three New Species

We use mitochondrial sequence data to identify divergent lineages within the gekkonid genus Cyrtodactylus in northeast India and use morphological data to describe six new species from within the Indo-Burma clade of Cyrtodactylus. The new species share an irregular colour pattern but differ from described species from the region in morphology and mitochondrial sequence data (>11 % uncorrected pairwise sequence divergence). Three new species are from along the Brahmaputra River and three are from mountains south of the Brahmaputra, including the largest Cyrtodactylus from India and the fifth gecko to be described from a major Indian city, Guwahati. 

Population Subdivision and Molecular Sequence Variation: Theory and Analysis of Drosophila ananassae Data

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1385-1395
Author(s):  
Claus Vogl ◽  
Aparup Das ◽  
Mark Beaumont ◽  
Sujata Mohanty ◽  
Wolfgang Stephan
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Allele Frequencies ◽  
Drosophila Ananassae ◽  
Population Subdivision ◽  
Variation Theory ◽  
Peripheral Populations ◽  
Molecular Variation ◽  
Data Set ◽  
Evolutionary Forces

Abstract Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter 0398; to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of 0398;, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

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