scholarly journals DNA barcoding mosquitoes: advice for potential prospectors

Parasitology ◽  
2018 ◽  
Vol 145 (5) ◽  
pp. 622-633 ◽  
Author(s):  
NIGEL W. BEEBE
Keyword(s):  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Dna Barcode ◽  
Nuclear Marker ◽  
Lineage Sorting ◽  
Mtdna Sequences ◽  
Closely Related Species ◽  
Pros And Cons ◽  
Species Groups ◽  
Coi Sequences

SUMMARYMosquitoes’ importance as vectors of pathogens that drive disease underscores the importance of precise and comparable methods of taxa identification among their species. While several molecular targets have been used to study mosquitoes since the initiation of PCR in the 1980s, its application to mosquito identification took off in the early 1990s. This review follows the research's recent journey into the use of mitochondrial DNA (mtDNA) cytochrome oxidase 1 (COI or COX1) as a DNA barcode target for mosquito species identification – a target whose utility for discriminating mosquitoes is now escalating. The pros and cons of using a mitochondrial genome target are discussed with a broad sweep of the mosquito literature suggesting that nuclear introgressions of mtDNA sequences appear to be uncommon and that the COI works well for distantly related taxa and shows encouraging utility in discriminating more closely related species such as cryptic/sibling species groups. However, the utility of COI in discriminating some closely related groups can be problematic and investigators are advised to proceed with caution as problems with incomplete lineage sorting and introgression events can result in indistinguishable COI sequences appearing in reproductively independent populations. In these – if not all – cases, it is advisable to run a nuclear marker alongside the mtDNA and thus the utility of the ribosomal DNA – and in particular the internal transcribed spacer 2 – is also briefly discussed as a useful counterpoint to the COI.

scholarly journals Improving the DNA Barcode Library of Mosquito Species With New Identifications and Discoveries in North-Central Argentina

2021 ◽  
Author(s):  
M Laurito ◽  
A M Ayala ◽  
D L Arias-Builes ◽  
W R Almirón
Keyword(s):  
Phylogenetic Relationships ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Dna Barcode ◽  
Lineage Sorting ◽  
North Central ◽  
Operational Taxonomic Units ◽  
Species Complexes ◽  
The Family ◽  
Geographical Scale

Abstract The family Culicidae is represented by 244 species in Argentina, many of them with epidemiological importance. DNA barcodes are effective tools for identifying mosquito species, for knowing genetic variability, and for establishing phylogenetic relationships. This work aims to explore mosquito diversity employing different species delimitation approaches and to establish formally a DNA barcode library for the Argentinian mosquito fauna. Barcode fragments of 80 specimens of Argentinian mosquitoes of 28 species of the genera Aedeomyia Theobald (Diptera: Culicidae), Anopheles Meigen (Diptera: Culicidae), Coquillettidia Dyar (Diptera: Culicidae), Culex L. (Diptera: Culicidae), Haemagogus Williston (Diptera: Culicidae), Mansonia Blanchard (Diptera: Culicidae), Nyssorhynchus Blanchard (Diptera: Culicidae), Ochlerotatus Lynch-Arribálzaga (Diptera: Culicidae), Psorophora Robinneau-Desvoidy (Diptera: Culicidae) and Uranotaenia Lynch-Arribálzaga (Diptera: Culicidae) were sequenced. Another 82 sequences were obtained from public databases to establish the phylogenetic relationships using Maximum Likelihood and Bayesian Inference, and the species boundaries based on three approaches (ABGD, GMYC, and mPTP). Sixteen of the 28 species sequenced were recovered as monophyletic, of which 12 were also recognized as molecular operational taxonomic units according to the three methodologies. The disparity between morphology and barcode-based identifications could be explained by synonymy, species complexes occurrence, hybridization, incomplete lineage sorting, or the effect of the geographical scale of sampling. Twenty of the 28 sequenced species are new barcodes for Argentina and 11 are the first for science. This increases from 31 to 52 (12.7 to 21.31%) and from six to 10 (28.57 to 47.62%) the number of species and genera, respectively, with barcode sequences in Argentina. New species records are provided.

scholarly journals A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

2019 ◽  
Vol 37 (4) ◽  
pp. 1211-1223 ◽  
Author(s):  
Tomáš Flouri ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent

Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

scholarly journals A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis

2019 ◽  
Author(s):  
Thomas Flouris ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Important Means

AbstractRecent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here we implement the multispecies-coalescent-with-introgression (MSci) model, an extension of the multispecies-coalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Re-analysis of datasets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

scholarly journals Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11843
Author(s):  
Carlos Prieto ◽  
Christophe Faynel ◽  
Robert Robbins ◽  
Axel Hausmann
Keyword(s):  
Incomplete Lineage Sorting ◽  
Dna Barcode ◽  
Morphological Data ◽  
Biological Assessment ◽  
Index Number ◽  
High Mountain ◽  
Lineage Sorting ◽  
Data Set ◽  
Index Numbers ◽  
The Mean

Background With about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in wing patterns. Geographic infraspecific variation is sometimes more substantial than variation between species. In this paper we present a large DNA barcode dataset of South American Lycaenidae. We analyze how well DNA barcode BINs match morphologically delimited species. Methods We compare morphology-based species identifications with the clustering of molecular operational taxonomic units (MOTUs) delimitated by the RESL algorithm in BOLD, which assigns Barcode Index Numbers (BINs). We examine intra- and interspecific divergences for genera represented by at least four morphospecies. We discuss the existence of local barcode gaps in a genus by genus analysis. We also note differences in the percentage of species with barcode gaps in groups of lowland and high mountain genera. Results We identified 2,213 specimens and obtained 1,839 sequences of 512 species in 90 genera. Overall, the mean intraspecific divergence value of CO1 sequences was 1.20%, while the mean interspecific divergence between nearest congeneric neighbors was 4.89%, demonstrating the presence of a barcode gap. However, the gap seemed to disappear from the entire set when comparing the maximum intraspecific distance (8.40%) with the minimum interspecific distance (0.40%). Clear barcode gaps are present in many genera but absent in others. From the set of specimens that yielded COI fragment lengths of at least 650 bp, 75% of the a priori morphology-based identifications were unambiguously assigned to a single Barcode Index Number (BIN). However, after a taxonomic a posteriori review, the percentage of matched identifications rose to 85%. BIN splitting was observed for 17% of the species and BIN sharing for 9%. We found that genera that contain primarily lowland species show higher percentages of local barcode gaps and congruence between BINs and morphology than genera that contain exclusively high montane species. The divergence values to the nearest neighbors were significantly lower in high Andean species while the intra-specific divergence values were significantly lower in the lowland species. These results raise questions regarding the causes of observed low inter and high intraspecific genetic variation. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the montane species concerned are relatively young and hybridization is probable. The release of our data set represents an essential baseline for a reference library for biological assessment studies of butterflies in mega diverse countries using modern high-throughput technologies an highlights the necessity of taxonomic revisions for various genera combining both molecular and morphological data.

scholarly journals Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids?

DNA Barcodes ◽  
2015 ◽  
Vol 3 (1) ◽  
Author(s):  
S. Behrens-Chapuis ◽  
F. Herder ◽  
H. R. Esmaeili ◽  
J. Freyhof ◽  
N. A. Hamidan ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Incomplete Lineage Sorting ◽  
Haplotype Sharing ◽  
Nuclear Marker ◽  
Lineage Sorting ◽  
Geographic Scale ◽  
Mitochondrial Coi ◽  
Wide Range ◽  
Taxonomic Uncertainty ◽  
Taxonomic Framework

AbstractDNA barcoding is a fast and reliable tool for species identification, and has been successfully applied to a wide range of freshwater fishes. The limitations reported were mainly attributed to effects of geographic scale, taxon-sampling, incomplete lineage sorting, or mitochondrial introgression. However, the metrics for the success of assigning unknown samples to species or genera also depend on a suited taxonomic framework. A simultaneous use of the mitochondrial COI and the nuclear RHO gene turned out to be advantageous for the barcode efficiency in a few previous studies. Here, we examine 14 cyprinid fish genera, with a total of 74 species, where standard DNA barcoding failed to identify closely related species unambiguously. Eight of the genera (Acanthobrama, Alburnus, Chondrostoma, Gobio, Mirogrex, Phoxinus, Scardinius, and Squalius) contain species that exhibit very low interspecific divergence, or haplotype sharing (12 species pairs) with presumed introgression based on mtCOI data. We aimed to test the utility of the nuclear rhodopsin marker to uncover reasons for the high similarity and haplotype sharing in these different groups. The included labeonine species belonging to Crossocheilus, Hemigrammocapoeta, Tylognathus and Typhlogarra were found to be nested within the genus Garra based on mtCOI. This specific taxonomic uncertainty was also addressed by the use of the additional nuclear marker. As a measure of the delineation success we computed barcode gaps, which were present in 75% of the species based on mtCOI, but in only 39% based on nuclear rhodopsin sequences. Most cases where standard barcodes failed to offer unambiguous species identifications could not be resolved by adding the nuclear marker. However, in the labeonine cyprinids included, nuclear rhodopsin data generally supported the lineages as defined by the mitochondrial marker. This suggests that mitochondrial patterns were not mislead by introgression, but are caused by an inadequate taxonomy. Our findings support the transfer of the studied species of Crossocheilus, Hemigrammocapoeta, Tylognathus and Typhlogarra to Garra.

scholarly journals Cryptic species diversity and reproductive isolation among sympatric lineages of Strongylocentrotus sea urchins in the northwest Atlantic

FACETS ◽  
2018 ◽  
Vol 3 (1) ◽  
pp. 61-78 ◽  
Author(s):  
Jason A. Addison ◽  
Jin-Hong Kim
Keyword(s):  
Reproductive Isolation ◽  
Cryptic Species ◽  
Sea Urchins ◽  
Incomplete Lineage Sorting ◽  
Strongylocentrotus Droebachiensis ◽  
Population Substructure ◽  
Nucleotide Polymorphisms ◽  
Lineage Sorting ◽  
Genetic Studies ◽  
Coi Sequences

Distinguishing between intra- and inter-specific variation in genetic studies is critical to understanding evolution because the mechanisms driving change among populations are expected to be different than those that shape reproductive isolation among lineages. Genetic studies of north Atlantic green sea urchins Strongylocentrotus droebachiensis (Müller, 1776) have detected significant population substructure and asymmetric gene flow from Europe to Atlantic Canada and interspecific hybridization between S. droebachiensis and Strongylocentrotus pallidus (Sars, 1871). However, combined with patterns of divergence at mtDNA sequences, morphological divergence at gamete traits suggests that the European and North American lineages of S. droebachiensis may be cryptic species. Here, we use a combination of cytochrome c oxidase subunit I ( COI) sequences and single nucleotide polymorphisms (SNPs) to test for cryptic species within Strongylocentrotus sea urchins and hybrids between S. droebachiensis and S. pallidus populations. We detect striking patterns of habitat and reproductive isolation between two S. droebachiensis lineages, with offshore deep-water collections consisting of S. pallidus in addition to a cryptic lineage sharing genetic similarity with previously published sequences from eastern Atlantic S. droebachiensis. We detected only limited hybridization among all three lineages of sea urchins, suggesting that shared genetic differences previously reported may be a result of historical introgression or incomplete lineage sorting.

scholarly journals Effectiveness of DNA Barcoding in Speyeria Butterflies at Small Geographic Scales

Diversity ◽  
2018 ◽  
Vol 10 (4) ◽  
pp. 130 ◽  
Author(s):  
Ryan Hill ◽  
Maya Ganeshan ◽  
Lindsay Wourms ◽  
Marcus Kronforst ◽  
Sean Mullen ◽  
...  
Keyword(s):  
San Francisco ◽  
Incomplete Lineage Sorting ◽  
San Francisco Bay Area ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Sympatric Species ◽  
Lineage Sorting ◽  
Bay Area ◽  
Wing Patterns ◽  
Conservation Concern

North American Speyeria butterflies are a group of conservation concern and a challenge to butterfly systematists. Establishing species delimitation and evolutionary relationships among Speyeria has proven difficult due to the polytypic nature of many species, coupled with the similarity of wing patterns of sympatric species. Recent molecular work has found not all Speyeria species to be monophyletic, which could be explained by improper species definitions, incomplete lineage sorting, or ongoing hybridization and introgression. However, these studies involved broad geographic sampling where molecular markers such as the DNA barcode may be especially subject to incomplete lineage sorting. Here we focus on a more local scale, analyzing the mitochondrial gene cytochrome oxidase subunit I (CoI) to test whether this marker recovers four sympatric Speyeria species: adiaste (W. H. Edwards, 1864), callippe (Boisduval, 1852), coronis (Behr, 1864), and zerene (Boisduval, 1852), in the greater San Francisco Bay Area. We found that CoI works well to separate all four species. Subspecies were less well-defined, with the S. adiaste subspecies clustering separately, but more mixed for the S. zerene and S. callippe subspecies. Overall, our analyses illustrate the utility of the DNA barcode for separating the Speyeria species and suggest further studies to investigate different geographic scales in order to elucidate genetic diversity patterns in this genus in North America.

scholarly journals Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus

2021 ◽  
Author(s):  
Olena Meleshko ◽  
Michael D Martin ◽  
Thorfinn Sand Korneliussen ◽  
Christian Schröck ◽  
Paul Lamkowski ◽  
...  
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Nuclear Genome ◽  
Lineage Sorting ◽  
Rapid Radiation ◽  
Organellar Genomes ◽  
Genome Wide ◽  
Phylogenetic Discordance ◽  
Species Groups ◽  
Open Question

Abstract The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by postspeciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.

scholarly journals Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia

2017 ◽  
Vol 18 (4) ◽  
pp. 1358-1366
Author(s):  
MOHD LUTFI ABDULLAH ◽  
SITI AZIZAH MOHD NOR ◽  
DARLINA MD. NAIM
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Incomplete Lineage Sorting ◽  
Molecular Taxonomy ◽  
Dna Barcode ◽  
Coi Gene ◽  
Lineage Sorting ◽  
Taxonomic Studies ◽  
Mitochondrial Cytochrome Oxidase ◽  
Blast Result

Abdullah ML, Nor SAM, Naim DMd. 2017. Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia. Biodiversitas 18: 1358-1366. The genus Ariidae contains many valuable fish species threatened by overfishing, but knowledge on distribution and threats is still limited due to taxonomic ambiguities. The aim of this study was to apply DNA barcoding techniques to establish a resource of DNA for identification of Ariidae species in Malaysia. A 621 bp of mitochondrial cytochrome oxidase subunit I (COI) gene was utilized to resolve phylogenetic relationships and molecular taxonomy of eight presumed Malaysian Ariid species. We found the monophyly of most species was well established with a mean Kimura-2 parameter (K2P) interspecies distance of 9.6% except for two species, Arius venosus, and Nemapteryx caelata that have very low interspecies genetic distance. The BLAST result shows only two species matched the presumably eight identified fish species. Such discrepancies could arise as a result of misidentifications or errors in GenBank database input, hybridization or incomplete lineage sorting. We suggest the use of DNA barcoding is integrated into the workflow during taxonomic studies as it could significantly increase knowledge about species distributions.

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