scholarly journals Molecular Analysis Reveals a High Diversity of Anopheline Mosquitoes in Yanomami Lands and the Pantanal Region of Brazil

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1995
Author(s):  
Teresa Fernandes Silva-do-Nascimento ◽  
Jordi Sánchez-Ribas ◽  
Tatiane M. P. Oliveira ◽  
Brian Patrick Bourke ◽  
Joseli Oliveira-Ferreira ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Indigenous Communities ◽  
Coi Gene ◽  
Single Linkage ◽  
Operational Taxonomic Units ◽  
As Species ◽  
Species Groups ◽  
Gene Data ◽  
Anopheline Mosquitoes ◽  
High Diversity

Identifying the species of the subfamily Anophelinae that are Plasmodium vectors is important to vector and malaria control. Despite the increase in cases, vector mosquitoes remain poorly known in Brazilian indigenous communities. This study explores Anophelinae mosquito diversity in the following areas: (1) a Yanomami reserve in the northwestern Amazon Brazil biome and (2) the Pantanal biome in southwestern Brazil. This is carried out by analyzing cytochrome c oxidase (COI) gene data using Refined Single Linkage (RESL), Assemble Species by Automatic Partitioning (ASAP), and tree-based multi-rate Poisson tree processes (mPTP) as species delimitation approaches. A total of 216 specimens collected from the Yanomami and Pantanal regions were sequenced and combined with 547 reference sequences for species delimitation analyses. The mPTP analysis for all sequences resulted in the delimitation of 45 species groups, while the ASAP analysis provided the partition of 48 groups. RESL analysis resulted in 63 operational taxonomic units (OTUs). This study expands our scant knowledge of anopheline species in the Yanomami and Pantanal regions. At least 18 species of Anophelinae mosquitoes were found in these study areas. Additional studies are now required to determine the species that transmit Plasmodium spp. in these regions.

Integrating DNA barcodes and morphology for species delimitation in theCorynoneuragroup (Diptera: Chironomidae: Orthocladiinae)

2013 ◽  
Vol 104 (1) ◽  
pp. 65-78 ◽  
Author(s):  
F.L. Silva ◽  
S. Wiedenbrug
Keyword(s):  
Dna Markers ◽  
Species Delimitation ◽  
Pupal Stage ◽  
Coi Gene ◽  
Morphological Divergence ◽  
Dna Barcodes ◽  
Morphological Criteria ◽  
Species Groups ◽  
Excellent Tool ◽  
Eleven Species

AbstractIn this study, we use DNA barcodes for species delimitation to solve taxonomic conflicts in 86 specimens of 14 species belonging to theCorynoneuragroup (Diptera: Chironomidae: Orthocladiinae), from the Atlantic Forest, Brazil. Molecular analysis of cytochrome c-oxidase subunit I (COI) gene sequences supported 14 cohesive species groups, of which two similar groups were subsequently associated with morphological variation at the pupal stage. Eleven species previously described based on morphological criteria were linked to DNA markers. Furthermore, there is the possibility that there may be cryptic species within theCorynoneuragroup, since one group of species presented internal grouping, although no morphological divergence was observed. Our results support DNA-barcoding as an excellent tool for species delimitation in groups where taxonomy by means of morphology is difficult or even impossible.

scholarly journals Species Delimitation of the Eisenia nordenskioldi Complex (Oligochaeta, Lumbricidae) Using Transcriptomic Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Sergei V. Shekhovtsov ◽  
Aleksandra A. Shipova ◽  
Tatiana V. Poluboyarova ◽  
Gennady V. Vasiliev ◽  
Elena V. Golovanova ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Coi Gene ◽  
Southeastern Part ◽  
Genetic Lineages ◽  
Transcriptomic Data ◽  
Its Phylogeny ◽  
Eisenia Nordenskioldi ◽  
Very High ◽  
Large Distribution ◽  
High Diversity

Eisenia nordenskioldi (Eisen, 1879) is the only autochthonous Siberian earthworm with a large distribution that ranges from tundra to steppe and broadleaved forests. This species has a very high morphological, ecological, karyological, and genetic diversity, so it was proposed that E. nordenskioldi should be split into several species. However, the phylogeny of the complex was unclear due to the low resolution of the methods used and the high diversity that should have been taken into account. We investigated this question by (1) studying the diversity of the COI gene of E. nordenskioldi throughout its range and (2) sequencing transcriptomes of different genetic lineages to infer its phylogeny. We found that E. nordenskioldi is monophyletic and is split into two clades. The first one includes the pigmented genetic lineages widespread in the northern and western parts of the distribution, and the second one originating from the southern and southeastern part of the species' range and representing both pigmented and non-pigmented forms. We propose to split the E. nordenskioldi complex into two species, E. nordenskioldi and Eisenia sp. 1 (aff. E. nordenskioldi), corresponding to these two clades. The currently recognized non-pigmented subspecies E. n. pallida will be abolished as a polyphyletic and thus a non-natural taxon, while Eisenia sp. 1 will be expanded to include several lineages earlier recognized as E. n. nordenskioldi and E. n. pallida.

scholarly journals Revision of the genus Callipia Guenée, 1858 (Lepidoptera, Geometridae), with the description of 15 new taxa

2018 ◽  
Author(s):  
Gunnar Brehm
Keyword(s):  
Host Plants ◽  
Molecular Genetic ◽  
Junior Synonym ◽  
Coi Gene ◽  
Valid Species ◽  
Threefold Increase ◽  
The Status ◽  
Species Groups ◽  
Gene Data ◽  
High Elevations

The vividly coloured Neotropical genus Callipia Guenée (1858) (Lepidoptera Linnaeus, 1758, Geometridae (Leach, 1815), Larentiinae (Leach, 1815), Stamnodini Forbes, 1948) is revised and separated into four species groups, according to a provisional phylogeny based on Cytochrome Oxidase I (COI) gene data and morphology. Fourteen new species are described using COI data and morphology: a) in the balteata group: C. fiedleri sp. nov., C. jakobi sp. nov., C. lamasi sp. nov.; b) in the vicinaria group: C. hausmanni sp. nov., C. walterfriedlii sp. nov.; c) in the parrhasiata group: C. augustae sp. nov., C. jonai sp. nov., C. karsholti sp. nov., C. levequei sp. nov., C. milleri sp. nov., C. sihvoneni sp. nov., C. wojtusiaki sp. nov. and d) in the constantinaria group: C. hiltae sp. nov., C. rougeriei sp. nov. One new subspecies is described: C. wojtusiaki septentrionalis subsp. nov. Two species are revived from synonymy: C. intermedia Dognin, 1914 stat. rev. and C. occulta Warren, 1904 stat. rev. The taxon hamaria Sperry, 1951 is transferred from being a junior synonym of C. constantinaria Oberthür, 1881 to being a junior synonym of C. occulta stat. rev. The taxon admirabilis Warren, 1904 is confirmed as being a junior synonym of C. paradisea Thierry-Mieg, 1904. The taxon languescens Warren, 1904 is confirmed as being a junior synonym of C. rosetta, Thierry-Mieg, 1904 and the taxon confluens Warren, 1905 is confirmed as being a junior synonym of C. balteata Warren, 1905. The status of the remaining species is not changed: C. aurata Warren, 1904, C. brenemanae Sperry, 1951, C. parrhasiata Guenée, 1858, C. flagrans Warren, 1904, C. fulvida Warren, 1907 and C. vicinaria Dognin. All here recognised 28 species are illustrated and the available molecular genetic information of 27 species, including Barcode Index Numbers (BINs) for most of the taxa is provided. The almost threefold increase from 10 to 28 valid species shows that species richness of tropical moths is strongly underestimated even in relatively conspicuous taxa. Callipia occurs from medium to high elevations in wet parts of the tropical and subtropical Andes from Colombia to northern Argentina. The early stages and host plants are still unknown.

scholarly journals Species delimitation of Margattea cockroaches from China, with seven new species (Blattodea, Ectobiidae, Pseudophyllodromiinae)

ZooKeys ◽  
2021 ◽  
Vol 1036 ◽  
pp. 121-151
Author(s):  
Jia-Jun He ◽  
Du-Ting Jin ◽  
Yi-Shu Wang ◽  
Yan-Li Che ◽  
Zong-Qing Wang
Keyword(s):  
New Species ◽  
Confidence Interval ◽  
Genetic Distance ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Operational Taxonomic Units ◽  
As Species ◽  
The Difference ◽  
Morphological Differences ◽  
Barcode Gap

Nearly 450 Margattea specimens were collected from 27 locations in China and their morphology was examined. Then 68 Margattea COI sequences were obtained and used to carry out phylogenetic analyses as well as species delimitation analyses using General Mixed Yule Coalescent (GMYC), Automatic Barcode Gap Discovery (ABGD), and Poisson Tree Processes (bPTP). GMYC analysis resulted in 21 molecular operational taxonomic units (MOTUs) (confidence interval: 20–22), which was completely consistent with the result of the bPTP. There were 15 MOTUs using the ABGD method. The number of MOTUs was slightly different from the assigned morphospecies (16). As to the incongruence between molecular and morphological results, we checked the specimens again and made sure that most morphological differences were determined to be intraspecific differences (except the difference between M. angusta and M. mckittrickae), although a large genetic distance existed. Finally, 16 Margattea species from China were defined in this study, of which, seven new species are established, i.e. Margattea deltodonta J-J He & Z-Q Wang, sp. nov., Margattea cuspidata J-J He & Z-Q Wang, sp. nov., Margattea caudata J-J He & Z-Q Wang, sp. nov., Margattea paratransversa J-J He & Z-Q Wang, sp. nov., Margattea disparilis J-J He & Z-Q Wang, sp. nov., Margattea transversa J-J He & Z-Q Wang, sp. nov., and Margattea bicruris J-J He & Z-Q Wang, sp. nov.

scholarly journals Revisiting the Diversity of Barbonymus (Cypriniformes, Cyprinidae) in Sundaland Using DNA-Based Species Delimitation Methods

Diversity ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 283
Author(s):  
Hadi Dahruddin ◽  
Arni Sholihah ◽  
Tedjo Sukmono ◽  
Sopian Sauri ◽  
Ujang Nurhaman ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Stock Assessment ◽  
Dna Barcode ◽  
Peninsular Malaysia ◽  
Reference Library ◽  
Tropical Regions ◽  
Operational Taxonomic Units ◽  
Inland Fisheries ◽  
Large Size ◽  
Species Groups

Biodiversity hotspots often suffer from a lack of taxonomic knowledge, particularly those in tropical regions. However, accurate taxonomic knowledge is needed to support sustainable management of biodiversity, especially when it is harvested for human sustenance. Sundaland, the biodiversity hotspot encompassing the islands of Java, Sumatra, Borneo, and Peninsular Malaysia, is one of those. With more than 900 species, its freshwater ichthyofauna includes a large number of medium- to large-size species, which are targeted by inland fisheries. Stock assessment requires accurate taxonomy; however, several species groups targeted by inland fisheries are still poorly known. One of those cases is the cyprinid genus Barbonymus. For this study, we assembled a consolidated DNA barcode reference library for Barbonymus spp. of Sundaland, consisting of mined sequences from BOLD, as well as newly generated sequences for hitherto under-sampled islands such as Borneo. A total of 173 sequences were analyzed using several DNA-based species delimitation methods. We unambiguously detected a total of 6 Molecular Operational Taxonomic Units (MOTUs) and were able to resolve several conflicting assignments to the species level. Furthermore, we clarified the identity of MOTUs occurring in Java.

scholarly journals Investigating the Parasitoid Community Associated with the Invasive Mealybug Phenacoccus solenopsis in Southern China

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 290
Author(s):  
Hua-Yan Chen ◽  
Hong-Liang Li ◽  
Hong Pang ◽  
Chao-Dong Zhu ◽  
Yan-Zhou Zhang
Keyword(s):  
Biological Control ◽  
Species Delimitation ◽  
Southern China ◽  
Insect Pest ◽  
Integrated Approach ◽  
Molecular Data ◽  
Coi Gene ◽  
Morphological Examination ◽  
Accurate Identification ◽  
Phenacoccus Solenopsis

The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), is an emerging invasive insect pest in China. Hymenopteran parasitoids are the key organisms for suppressing populations of P. solenopsis in the field, and therefore could be used as biological agents. Accurate identification of the associated parasitoids is the critical step to assess their potential role in biological control. In this study, we facilitated the identification of the parasitoid composition of P. solenopsis using an integrated approach of species delimitation, combining morphology with molecular data. Eighteen Hymenoptera parasitoid species belonging to 11 genera of four families are recognized based on morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene and the 28S rDNA using the automatic barcode gap discovery (ABGD) and the Bayesian Poisson tree processes model (bPTP). Among these species, eight species are primary parasitoids with Aenasius arizonensis (Girault) (Hymenoptera: Encyrtidae) being the dominant taxon, while the other 10 species are probably hyperparasitoids, with a prevalence of Cheiloneurus nankingensis Li & Xu (Hymenoptera: Encyrtidae). These results indicate that parasitoid wasps associated with P. solenopsis from China are diverse and the integrated taxonomic approach applied in this study could enhance the accurate identification of these parasitoids that should be assessed in future biological control programs.

scholarly journals High Diversity of Magnetotactic Deltaproteobacteria in a Freshwater Niche

2013 ◽  
Vol 79 (8) ◽  
pp. 2813-2817 ◽  
Author(s):  
Yinzhao Wang ◽  
Wei Lin ◽  
Jinhua Li ◽  
Yongxin Pan
Keyword(s):  
Magnetotactic Bacteria ◽  
Natural Environments ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Geological Processes ◽  
Freshwater Site ◽  
High Diversity

ABSTRACTKnowledge of the diversity of magnetotactic bacteria in natural environments is crucial for understanding their contribution to various biological and geological processes. Here we report a high diversity of magnetotactic bacteria in a freshwater site. Ten out of 18 operational taxonomic units (OTUs) were affiliated with theDeltaproteobacteria. Some rod-shaped bacteria simultaneously synthesized greigite and magnetite magnetosomes.

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 Swarm v2: highly-scalable and high-resolution amplicon clustering

2015 ◽  
Author(s):  
Frédéric Mahé ◽  
Torbjørn Rognes ◽  
Christopher Quince ◽  
Colomban de Vargas ◽  
Micah S Dunthorn
Keyword(s):  
High Resolution ◽  
Initial Phase ◽  
Computation Time ◽  
Two Dimensional ◽  
Fine Scale ◽  
Single Linkage ◽  
Fasta Format ◽  
Operational Taxonomic Units ◽  
Abundant Otus ◽  
Local Clustering

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2 that has two important novel features: 1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and 2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

Multi-instar descriptions of cave dwelling Erythraeidae (Trombidiformes: Parasitengona) employing an integrative approach

Zootaxa ◽  
2019 ◽  
Vol 4717 (1) ◽  
pp. 137-184 ◽  
Author(s):  
SAMUEL GEREMIAS DOS SANTOS COSTA ◽  
HANS KLOMPEN ◽  
LEOPOLDO FERREIRA DE OLIVEIRA BERNARDI ◽  
LUCIANA CARDOSO GONÇALVES ◽  
DANTE BATISTA RIBEIRO ◽  
...  
Keyword(s):  
Life Cycle ◽  
Cytochrome Oxidase ◽  
Molecular Analysis ◽  
Species Delimitation ◽  
Morphological Changes ◽  
Molecular Data ◽  
Coi Gene ◽  
Integrative Approach ◽  
Larval Instars ◽  
Individual Host

The life cycle of Parasitengona includes major morphological changes precluding an instar association based only on the morphology. This makes rearing and/or molecular data necessary to associate the heteromorphic instars. Most of the described species are known from either post larval instars or larva. Following a previous study on Palearctic Erythraeidae, in the present study the instar association was made through an integrative approach including rearing trials and molecular analysis of the cytochrome oxidase I (COI) gene with the Bayesian Generalized Mixed Yule Coalescent (bGMYC) algorithm for species delimitation. Two new cave dwelling Erythraeidae (Trombidiformes: Parasitengona) species are described Lasioerythraeus jessicae sp. nov. and Leptus sidorchukae sp. nov. including all active instars. Additionally, a complete description of the previously unknown adults of Charletonia rocciai Treat & Flechtmann, 1979 is provided with notes on the larva and deutonymph. We also demonstrate experimentally that Ch. rocciai larvae are not attached to the same individual host during the entire feeding stage. We discuss the presence of troglomorphisms in Le. sidorchukae sp. nov.; and the distribution of the species. 

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