Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae)

Schwarzfeld, Marla D.; Sperling, Felix A. H.

doi:10.1016/j.ympev.2015.08.003

Cited by 37 publications

(49 citation statements)

References 135 publications

(101 reference statements)

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“…The combination of multiple delineation approaches provided confidence in proposed MOTU estimates. Within single loci, we found perfect congruence between the coalescent‐based GMYC and the ABGD method, and, in line with other studies, only slight differences in levels of diversity (e.g., Puillandre et al ., ; Hendrixson et al ., ; Schwarzfeld & Sperling, ). The Bayesian method BPP further supported our best MOTU hypothesis but was unable to rule out uncertainty as the model entailed specification of a pre‐defined species tree (Satler, Carstens & Hedin, ).…”

Section: Discussionmentioning

confidence: 99%

“…Because of their fundamentally different statistical approach comparing the results of both methods can increase or limit confidence in those results (e.g., Ratnasingham & Hebert, 2013). Based on simulations and empirical data, GMYC is considered a robust delimitation tool (Fujisawa & Barraclough, 2013;Schwarzfeld & Sperling, 2015), but some studies indicate that GMYC has problems with over splitting evolutionary lineages in cases where fewer than 20% of demes are sampled (Lohse, 2009;Papadopoulou et al, 2009). Thus, we used the Bayesian species delineation approach BPP to validate the MOTU hypothesis resulting from GMYC and ABGD analyses.…”

Section: Molecular Data Analysesmentioning

confidence: 99%

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Environmental and spatial characterisation of an unknown fauna using DNA sequencing – an example with Himalayan Hydropsychidae (Insecta: Trichoptera)

Hoppeler

Shah

et al. 2016

Freshwater Biology

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Summary Ecological studies of freshwater biota in understudied regions are often obstructed by poor taxonomic knowledge. We posit that molecular tools can help alleviate this issue and present an example where we combined molecular tools, environmental data and ecological statistics to investigate the distribution and community ecology of an unknown fauna of hydropsychid caddisflies along altitudinal gradients in four Himalayan river systems of Central and Eastern Nepal. A total of 484 larval specimens from 34 tributaries were examined. Phylogenetic analysis of the mitochondrial cytochrome c oxidase I (COI) and the nuclear ribosomal RNA 28S were used to delineate molecular operational taxonomic units (MOTUs) applying three analytical methods: general mixed Yule‐coalescent (GMYC) model, Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics and Phylogeography (BPP). Spatial distributional patterns and potential differences in ecological niches among MOTUs were statistically tested using regression and correlation approaches. Further, we examined the data for signs of non‐random structure in MOTU communities. MOTU diversity within the family of Hydropsychidae was generally high but varied across evaluated gene fragments and slightly among delineation methods. Yet, the subsequent evaluation of environmental and spatial drivers and resulting distributional patterns were highly consistent among the different MOTU estimates. Within each river system, we found community composition varied greatly along the altitudinal gradients, with many MOTUs associated with specific altitudinal ranges. Prevalent MOTU turnover at the river system scale indicated high β‐diversity in the hydropsychid community leading to high degrees of regional endemism. In the Langtang river system, we found fewer MOTU co‐occurrences than expected by chance. These results highlight the utility of DNA‐based approaches using variable genetic markers (mitochondrial or ribosomal nuclear) for primary biodiversity assessment of poorly studied groups or regions. Our study further shows that DNA‐based biodiversity measures are suitable for downstream applications, such as exploring fundamental questions in stream ecology.

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Section: Discussionmentioning

confidence: 99%

Section: Molecular Data Analysesmentioning

confidence: 99%

Environmental and spatial characterisation of an unknown fauna using DNA sequencing – an example with Himalayan Hydropsychidae (Insecta: Trichoptera)

Hoppeler

Shah

et al. 2016

Freshwater Biology

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“…The input tree was an ML tree constructed by RAxML with GTRCAT model. However, we encountered the same problem as Schwarzfeld and Sperling (2015), namely that the bPTP analysis failed to show convergence under 500,000 generations (the upper limit of the web server). Therefore, only the PTP result is displayed and discussed below.…”

Section: Methodsmentioning

confidence: 99%

DNA barcoding and species delimitation of Chaitophorinae (Hemiptera, Aphididae)

Zhu¹,

Chen²,

Chen³

et al. 2017

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Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process). The genetic interspecific divergence was clearly larger than the intraspecific divergence for four molecular markers. COI and COII genes were found to be more suitable for Chaitophorinae DNA barcoding. For species delimitation, at least one distance-based method combined with one tree-based method would be preferable. Based on the data for Chaitophorus saliniger and Laingia psammae, DNA barcoding may also reveal geographical variation.

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“…The only input parameter, although imprecisely, was the maximum prior intraspecific distance, p . We chose ABGD instead of bPTP [53] or GMYC [54] because this method was independent of phylogenetic trees and particularly sensitive to recent speciation events [55]. This analysis was performed on the ABGD website (http://wwwabi.snv.jussieu.fr/public/abgd/abgdweb.html) and used the 674 CYT B sequences as input data (Table 2).…”

Section: Methodsmentioning

confidence: 99%

Multi-locus phylogeny using topotype specimens sheds light on the systematics of Niviventer (Rodentia, Muridae) in China

Zhang

Wan

et al. 2016

BMC Evol Biol

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Background Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4). We estimated phylogenetic relationships on the basis of one mitochondrial and three nuclear genes, using concatenation and coalescent-based approaches. We also employed molecular species delimitation approaches to test the existence of cryptic and putative new species.ResultsOur phylogeny was finely resolved, especially for the N. confucianus-like species. Our data provided the first support for N. brahma and N. eha as sister species, an assignment that is congruent with their morphological similarities. Species delimitation analyses provided new insight into species diversity and systematics. Three geographic populations of N. confucianus and one of N. fulvescens were supported as genetically distinct in our species delimitation analyses, while three recognized species (N. coninga, N. huang, and N. lotipes) were not strongly supported as distinct.ConclusionsOur results suggested that several genetically distinct species may be contained within the species currently known as N. confucianus and N. fulvescens. In addition, the results of Bayesian Phylogenetics and Phylogeography (BPP) for N. coninga, N. huang, and N. lotipes indicated that either inter-specific gene flow had occurred or imperfect taxonomy was present. Morphological examinations and morphometric analyses are warranted to examine the molecular results.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0832-8) contains supplementary material, which is available to authorized users.

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Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae)

Cited by 37 publications

References 135 publications

Environmental and spatial characterisation of an unknown fauna using DNA sequencing – an example with Himalayan Hydropsychidae (Insecta: Trichoptera)

Environmental and spatial characterisation of an unknown fauna using DNA sequencing – an example with Himalayan Hydropsychidae (Insecta: Trichoptera)

DNA barcoding and species delimitation of Chaitophorinae (Hemiptera, Aphididae)

Multi-locus phylogeny using topotype specimens sheds light on the systematics of Niviventer (Rodentia, Muridae) in China

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