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      Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)

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          Abstract

          The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods).

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          Cryptic species as a window on diversity and conservation.

          The taxonomic challenge posed by cryptic species (two or more distinct species classified as a single species) has been recognized for nearly 300 years, but the advent of relatively inexpensive and rapid DNA sequencing has given biologists a new tool for detecting and differentiating morphologically similar species. Here, we synthesize the literature on cryptic and sibling species and discuss trends in their discovery. However, a lack of systematic studies leaves many questions open, such as whether cryptic species are more common in particular habitats, latitudes or taxonomic groups. The discovery of cryptic species is likely to be non-random with regard to taxon and biome and, hence, could have profound implications for evolutionary theory, biogeography and conservation planning.
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            The general stochastic model of nucleotide substitution.

            DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
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              Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus).

              Being able to efficiently and accurately delimit species is one of the most basic and important aspects of systematics because species are the fundamental unit of analysis in biogeography, ecology, and conservation. We present a rationale and approach for combining ecological niche modeling, spatially explicit analyses of environmental data, and phylogenetics in species delimitation, and we use our methodology in an empirical example focusing on Aneides flavipunctatus, the black salamander (Caudata: Plethodontidae), in California. We assess the relationships between genetic, environmental, and geographic distance among populations. We use 11 climatic variables and point locality data from public databases to create ecological niche models. The suitability of potential contact zones between parapatric lineages is also assessed using the data from ecological niche modeling. Phylogenetic analyses of portions of the mitochondrial genome reveal morphologically cryptic mitochondrial lineages in this species. In addition, we find that patterns of genetic divergence are strongly associated with divergence in the ecological niche. Our work demonstrates the ease and utility of using spatial analyses of environmental data and phylogenetics in species delimitation, especially for groups displaying fine-scaled endemism and cryptic species.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                17 August 2016
                2016
                : 11
                : 8
                : e0160001
                Affiliations
                [1 ]Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
                [2 ]Laboratory for Biosystems Research, BioSense Institute—Research Institute for Information Technologies in Biosystems, University of Novi Sad, Novi Sad, Serbia
                [3 ]Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
                Queensland University of Technology, AUSTRALIA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceived and designed the experiments: LŠ JA AV.

                • Performed the experiments: LŠ JA AV.

                • Analyzed the data: LŠ JA AV DM.

                • Contributed reagents/materials/analysis tools: AV GS.

                • Wrote the paper: LŠ JA AV GS MĐ SR DM DO.

                Author information
                http://orcid.org/0000-0003-1616-2701
                Article
                PONE-D-16-15001
                10.1371/journal.pone.0160001
                4988715
                27532618
                5c41813d-093f-4a4c-a13f-f5d8e88bdbf3
                © 2016 Šašić et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 13 April 2016
                : 12 July 2016
                Page count
                Figures: 13, Tables: 5, Pages: 27
                Funding
                This work was supported by the Ministry of Education, Science and Technological Development of Serbia ( http://www.mpn.gov.rs/), Grant Number 173002 (Conservation strategies for the preservation of protected and strictly protected species in Serbia—hoverflies (Insecta: Diptera: Syrphidae) as model organisms); AV. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Ecology
                Ecological Niches
                Ecology and Environmental Sciences
                Ecology
                Ecological Niches
                Biology and Life Sciences
                Taxonomy
                Computer and Information Sciences
                Data Management
                Taxonomy
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Species Delimitation
                Research and Analysis Methods
                Imaging Techniques
                Morphometry
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Cryptic Speciation
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Phylogenetic Analysis
                Research and Analysis Methods
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Phylogenetic Analysis
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Haplotypes
                Biology and Life Sciences
                Genetics
                Population Genetics
                Haplotypes
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Haplotypes
                Biology and Life Sciences
                Taxonomy
                New Species Reports
                Computer and Information Sciences
                Data Management
                Taxonomy
                New Species Reports
                Custom metadata
                All relevant data are within the paper and its Supporting Information files. Newly generated DNA sequences are available in GenBank under accession numbers KU365419-365471 and KU365483-365535.

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                Uncategorized

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