Multi‐locus species delimitation in closely related animals and fungi: one marker is not enough

Dupuis, Julian R.; Roe, Amanda D.; Sperling, Felix A. H.

doi:10.1111/j.1365-294x.2012.05642.x

Cited by 275 publications

(224 citation statements)

References 176 publications

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“…This approach is often used as an alternative to morphological and biological species recognition (Dettman et al 2003a). However, there have been relatively a few evaluations of the utility of genes to delineate closely related species in genera with broad host ranges and wide geographic distributions (Giraud et al 2008;Dupis et al 2012;Groenewald et al 2013;Wikee et al 2013;Salgado-Salazar et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

et al. 2014

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The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the generic type species Diaporthe eres has been uncertain due to the lack of ex-type cultures. Species limits of D. eres and closely related species were evaluated using molecular phylogenetic analysis of eight genes including nuclear ribosomal internal transcribed spacer (ITS), partial sequences of actin (ACT), DNA-lyase (Apn2), translation elongation factor 1-α (EF1-α), beta-tubulin (TUB), calmodulin (CAL), 60s ribosomal protein L37 (FG1093) and histone-3 (HIS). The occurrence of sequence heterogeneity of ITS within D. eres is observed, which complicates the analysis and may lead to overestimation of the species diversity. The strict criteria of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) were applied to resolve species boundaries based on individual and combined analyses of other seven genes except the ITS. We accept nine distinct phylogenetic species including helicis and D. pulla. Modern descriptions and illustrations are provided for these species. Newly designed primers are introduced to amplify and sequence the Apn2 (DNA-lyase) gene in Diaporthe. Based on phylogenetic informativeness profiles, EF1-α, Apn2 and HIS genes are recognised as the best markers for defining species in the D. eres complex.

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Section: Introductionmentioning

confidence: 99%

Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

et al. 2014

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“…In the animal kingdom, mitochondrial DNA (mtDNA) is one of the most popular markers because of its many ideal properties (Galtier et al 2009). Although mtDNA is proved to be suitable for barcoding animal life and highly informative in phylogenetic and phylogeographic studies, mtDNA patterns do not always reflect the real evolutionary history of the studied species and may be incongruent with nuclear data (Dupuis et al 2012). Low intraspecific mtDNA variation can make it impossible to reveal the phylogeography of focal groups of organisms.…”

Section: Introductionmentioning

confidence: 99%

Controversial patterns of Wolbachia infestation in the social parasitic Maculinea butterflies (Lepidoptera: Lycaenidae)

et al. 2015

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Wolbachia is a common group of intracellular bacteria found in arthropods and filarial nematodes. Since the past decade they have attracted considerable interest owing to their various effects on hosts, which range from reproductive manipulation to mutualism. Moreover, they can influence the mitochondrial DNA pattern which do not reflect the real evolutionary history of the target species and may be incongruent with nuclear data.Previously Wolbachia-manipulated mtDNA patterns, namely mito-nuclear discordance and deep mitochondrial splits associated with specific Wolbachia infections have been also discovered in the genus Maculinea. Here we present a comprehensive study on Wolbachia infestation and the genetic diversity of all Maculinea species in the Carpathian Basin. The prevalence and the pattern of the infestation highly differ among Maculinea species. M. alcon and M. arion are infected in 100%, each of these species with a single strain, but the infection level of M. nausithous and M. teleius is much lower, additionally, they are infected with multiple strains. The genetic diversity of Maculinea species proved to be generally low, only M. nausithous showed geographic pattern based on mitochondrial sequences and allozymes. In contrast with the previous studies, we could not detect mitonuclear discordance or find evidence for Wolbachia-induced selective sweep. Based on our results, we cannot hold only Wolbachia responsible for the restricted genetic diversity of Maculinea in the Carpathian Basin.Probably several factors shape together the level and pattern of genetic variability in Maculinea butterflies.

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“…The lower taxonomic level relationships have been resolved using the ITS2 of the nuclear rDNA gene cluster (Wyngaard et al 2010). Combine with mitochondrial genes and nucleic genes would produce more reliable species description than those based on a single gene (Dupuis et al 2012). One of the candidate nuclear marker is the small nuclear subunit of the ribosomal RNA ( rRNA) gene, which is a common molecular marker frequently used in phylogenetic studies ( Kruger et al 2012, Petrov et al 2014, Fonseca et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic information of freshwater copepod (Diaptomus sicilis) with special reference to 18S rRNA

Mookkaiah

Ramanibai

2016

IJBR

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In the present investigation to isolate freshwater calanoid copepods (Diaptomus sicilis) was characterized and identify the organisms by 18S rRNA sequencing. Plankton samples containing D. sicilis were collected during January 2014 (Post-monsoon) from Madippakkam Lake (12°57'41"N80°11'27"E) Chennai, Tamil Nadu. Immediately after sampling, specimens for genetic analyses were fixed in 95% ethyl alcohol. The total DNA was extracted from the individual copepod D. sicilis using Qiagen Blood tissue kit. The nuclear small subunit 18S rRNA gene was amplified using the Universal primer LCO -1490 (5'-GGTCAACAAATCATAAAGATATTGG-3') and HCO-2198 (5'-TAAACTTCAGGGTGACCAAAAAATCA-3'). PCR products were loaded onto a 1% TAE agarose gel. Sequences were carried out an automated sequencer. The nucleotide sequence of 1282 base pair region of 18S rRNA was determined for D. sicilis. The similarity of sequences of D. sicilis was retrieved by BLASTn program and maximum identity and E-value was 76% and 0.00, respectively. The PCR products of D. sicilis individuals showed 80% similarity with the partial nuclear small subunit 18S rRNA gene region of other calanoid copepods. Based on molecular data the freshwater Calanoid copepods showed different algorithms and similar types of topologies useful for designing molecular analyses using phylogeny tree construction.Present molecular studies on the relationship of D. sicilis with other freshwater calanoid copepods indicate that this species is close to D. castor followed by D. keniraensis.

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Multi‐locus species delimitation in closely related animals and fungi: one marker is not enough

Cited by 275 publications

References 176 publications

Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

Controversial patterns of Wolbachia infestation in the social parasitic Maculinea butterflies (Lepidoptera: Lycaenidae)

Phylogenetic information of freshwater copepod (Diaptomus sicilis) with special reference to 18S rRNA

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