ASAP: assemble species by automatic partitioning

Molecular Ecology Resources, Год журнала: 2020, Номер 21(2), С. 609 - 620

Опубликована: Окт. 15, 2020

Abstract Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough split sets as large 10 4 sequences into putative in several minutes. Although grounded evolutionary theory, the implementation of hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding computational burden phylogenetic reconstruction. Importantly, proposes ranked scoring system no biological prior insight intraspecific diversity. stand‐alone program can be used either through graphical web‐interface or downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP GMYC) on real COI representing various degrees challenge (from small easy cases complicated also Monte‐Carlo simulations multispecies coalescent framework assess strengths weaknesses other programs. Through these analyses, demonstrate has potential become major tool taxonomists it rapidly full exploratory interface relevant hypothesis first step integrative taxonomy process.

Язык: Английский

---

Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo

Bioinformatics, Год журнала: 2017, Номер 33(11), С. 1630 - 1638

Опубликована: Янв. 20, 2017

In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast discovery biodiversity estimates. Among those, distance-based the most common choice scale well with large datasets; however, sensitive to similarity threshold parameters ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is phylogeny-aware that does not rely on such thresholds. Yet, two weaknesses PTP impact its accuracy practicality when applied it account divergent intraspecific variation slow number sequences.We introduce multi-rate (mPTP), an improved alleviates theoretical technical shortcomings PTP. It incorporates different levels genetic diversity deriving from differences either history or sampling each species. Results empirical data suggest mPTP superior popular it, consistently yields more accurate delimitations respect taxonomy (i.e., identifies taxonomic species, infers numbers closer taxonomy). Moreover, require any input. novel dynamic programming algorithm attains speedup at least five orders magnitude compared PTP, allowing delimit (meta-) barcoding data. addition, Markov Chain Monte Carlo provides comprehensive evaluation inferred just few seconds millions steps, independently tree size.mPTP implemented C available download http://github.com/Pas-Kapli/mptp under GNU Affero 3 license. A web-service http://mptp.h-its.org .: [email protected] [email protected] [email protected] Bioinformatics online.

Язык: Английский

---

What are fungal species and how to delineate them?

Fungal Diversity, Год журнала: 2021, Номер 109(1), С. 1 - 25

Опубликована: Июль 1, 2021

Язык: Английский

---

Cryptic species in the nuisance midge Polypedilum nubifer (Skuse (Diptera: Chironomidae) and the status of Tripedilum Kieffer

Zootaxa, Год журнала: 2016, Номер 4079(4)

Опубликована: Фев. 15, 2016

Polypedilum nubifer (Skuse, 1889), originally described from Australia, is an apparently widespread species of Chironomidae (Diptera) that can attain nuisance densities in some eutrophic water bodies. Appropriate management depends upon the identity and ability to distinguish potential cryptic taxa. A morphological study larvae, pupae adults both sexes confirmed P. as widely distributed frequently abundant, but also revealed two previously limited distribution northern Australia. These are new illustrated all stages here. quasinubifer Cranston sp. n. north-west Queensland, Australia Thailand Singapore. paranubifer known only retention ponds a uranium mine Northern Territory, Unusual features including alternate Lauterborn organs on larval antenna, cephalic tubules pupa frontal tubercles adult head present well. Newly slide-mounted types pelostolum Kieffer, 1912 (lectotype designated here) confirm synonymy Chironomus Skuse, 1889, examined newly-slide mounted types. Reviewed plus evidence does not support recognition Tripedilum 1921 separate taxon; therefore, returned junior with s. str.

Язык: Английский

---

Testing the Global Malaise Trap Program – How well does the current barcode reference library identify flying insects in Germany?

Biodiversity Data Journal, Год журнала: 2016, Номер 4, С. e10671 - e10671

Опубликована: Дек. 1, 2016

Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time space crucial for efficient successful management of ecosystem services, as well predicting change. To better understand diversity patterns, Germany participated the Global Malaise Trap Program, a world-wide collection program arthropods using this sampling method followed by their DNA barcode analysis. Traps were deployed at two localities: "Nationalpark Bayerischer Wald" Bavaria, largest terrestrial Natura 2000 area Germany, nature conservation Landskrone, an EU habitats directive site Rhine Valley. Arthropods collected from May September track taxonomic temporal succession these locations.In total, 37,274 specimens sorted barcoded, resulting 5,301 different genetic clusters (BINs, Barcode Index Numbers, proxy species) with just 7.6% BINs shared. Accumulation curves BIN count versus number analyzed suggest that about 63% potential sites was recovered single season sampling. Diversity both rose (496 & 565 BINs) July (1,236 1,522 before decreasing (572 504 BINs). Unambiguous names assigned 35% (1,868) which represented 12,640 specimens. Another 7% (386) 1,988 genus, while 26% (1,390) 12,092 only placed family. These results illustrate how comprehensive reference library can identify unknown specimens, but also reveal is constrained gaps quantity quality records BOLD, especially Hymenoptera Diptera. As voucher available morphological study, we invite experts assist identification unnamed BINs.

Язык: Английский

---

Algorithmic single‐locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles

Molecular Ecology Resources, Год журнала: 2016, Номер 17(3), С. 393 - 404

Опубликована: Июнь 13, 2016

Abstract The vast number of undescribed species and the fast rate biodiversity loss call for new approaches to speed up alpha taxonomy. A plethora methods delimiting or operational taxonomic units ( OTU s) based on sequence data have been published in recent years. We test ability four delimitation BIN , ABGD GMYC PTP ) reproduce established boundaries a carefully curated DNA barcode set 1870 North European beetle species. also explore how sampling effort, intraspecific variation, nearest neighbour divergence nonmonophyly affect delimitations. All produced approximately 90% identity between s. effects variation differed methods. was sensitive singleton sequences, while showed tendencies oversplitting. best fit s achieved using simple rules find consensus discordant Using several simultaneously allows compensate each other's weaknesses. Barcode‐based ‐picking is an efficient way delimit putative from large sets where use more sophisticated multilocus genomic not feasible.

Язык: Английский

---

Large‐scale DNA‐based survey of frogs in Amazonia suggests a vast underestimation of species richness and endemism

Journal of Biogeography, Год журнала: 2020, Номер 47(8), С. 1781 - 1791

Опубликована: Май 18, 2020

Abstract Aim Mapping Amazonian biodiversity accurately is a major challenge for integrated conservation strategies and to study its origins. However, species boundaries their respective distribution are notoriously inaccurate in this region. Here, we generated georeferenced database of short mtDNA sequences from frogs, revised the richness delimitation bioregions Eastern Guiana Shield estimated endemism within these bioregions. Location Amazonia, with focus on Shield. Taxon studied Amphibia: Anura. Methods We used an extensive DNA‐based sampling anuran amphibians Amazonia using next‐generation sequencing delimit Operational Taxonomic Units (OTU) distribution. analysed infer Latent Dirichlet Allocation modelling. then compared based our results current IUCN database, inferred environmental variables that contributed most biogeographic pattern. Results The recognized focal area increased 440 currently listed by Red List as much 876 OTUs dataset. recovered eight bioregions, among which three lie up 82% found endemic, figure times higher than previous estimate (28%). Environmental features related seasonal precipitations identified playing important role shaping amphibian Main conclusions Our have implications defining future priorities vast given vastly underestimated, might therefore hide large portion threatened species. Moreover, findings raise concern about meta‐analyses public databases dealing poorly known groups.

Язык: Английский

---

DNA barcoding of Chironomidae from the Lake Skadar region: Reference library and a comparative analysis of the European fauna

Diversity and Distributions, Год журнала: 2022, Номер 28(12), С. 2838 - 2857

Опубликована: Март 16, 2022

Abstract Aims The main aim of this study was to fill a gap in barcoding data the European Chironomidae Balkan region, developing and testing efficiency reference DNA barcode library for ancient Lake Skadar basin species (Montenegro/Albania), region Europe never before subjected studies on Chironomidae. Another test identification Chironomidae, including estimation optimal thresholds, using >12,000 barcodes. Location adjacent area (Montenegro/Albania). Methods Through study, 770 individuals from were barcoded, both at adult pre‐imaginal stages. Adults morphologically identified, while larvae assigned by molecular identification, different methods, which tested, total 97 barcoded species. Results dataset developed 98.6%, value line with that obtained when evaluated (95.8%), confirms accuracy these insects. Moreover, we found threshold family is 1.6% nucleotide distance, though more specific thresholds are suggested belonging subfamilies, since they related lower errors than use general threshold. analysis inconsistency between morphological shed light taxonomic issues within Previously postulated synonyms confirmed, also further cases requiring deeper investigation detected. Main conclusions Our de novo shown have high efficiency. Taxon‐specific increase efficacy identification. Hypothesized could be validated through techniques.

Язык: Английский

---

Analysis of DNA cox1 barcoding revealed novel haplotype in Schistosoma haematobium isolated from Western Sudan

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Янв. 15, 2025

Schistosomiasis poses a significant global health threat, particularly in tropical and subtropical regions like Sudan. Although numerous epidemiological studies have examined schistosomiasis Sudan, the genetic diversity of Schistosoma haematobium populations, specifically through analysis mtcox1 gene, remains unexplored. This study aimed to investigate risk factors associated with urogenital among school pupils El-Fasher, Western as well human S. this region. A cross-sectional was conducted aged 4 19 years. In total, 196 urine samples fecal were collected from participants across schools, centers, refugee camps El-Fasher. Samples using simple centrifugation/sedimentation technique formol-ether concentration method detect mansoni eggs, respectively. partial gene amplified sequenced by Sanger technique. neighbor-joining phylogenetic tree generated MEGA software, haplotype network constructed PopART v.1.7 median-joining method. study, detected 6.1% (12/196) while no ova observed samples. The infection more common those who relied on indirect water supply tankers (6, 50%). No residents camps. Only eight PCR-positive, which successfully sequenced, included analysis. unique (Hap_1) sequence found cox1 sequences El-Fasher strains. Both Gezira (Hap_31) fall within mainland Africa group (group 1). conclusion, identified novel strain provides insights into evolutionary history phylogeography western data could help control monitoring For first time, we utilized DNA barcoding haplotypes

Язык: Английский

---

DNA barcodes successfully delimit morphospecies in a superdiverse insect genus

Zoologica Scripta, Год журнала: 2018, Номер 47(3), С. 311 - 324

Опубликована: Март 30, 2018

Polypedilum Kieffer (Diptera: Chironomidae), with 520 currently known species worldwide, can be extremely difficult to identify level based on the morphology. We used 3,670 cytochrome c oxidase subunit I (COI) barcodes explore efficiency of COI differentiate between in a superdiverse aquatic insect genus. The Barcode Life Data System (BOLD) presented 286 BIN clusters , representing 163 morphospecies, which 93 were contributed from our laboratory. Molecular operational taxonomic units (OTUs) ranged 158 345, Automatic Gap Discovery (ABGD), Index Number (BIN), Bayesian Poisson tree processes (bPTP), generalized mixed Yule coalescent (GMYC), jMOTU, multi‐rate (mPTP), neighbor‐joining (NJ) and prethreshold clustering. In comparison, GMYC, bPTP, mPTP suggested more than warranted by morphology, while ABGD, NJ, clustering ABGD yielded conservative number when setting higher thresholds. Nine complexes deep intraspecific divergences indicated 18 potentially cryptic species, require further research including complete life histories nuclear genetic data resolved. discrimination DNA proved successful 94.4% all studied morphological species.

Язык: Английский

---