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      Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees

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          Abstract

          Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs) using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC) models and Poisson-tree-process (PTP) models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and genetic groups show little agreement, which may help to explain the lack of agreement among previous taxonomic revisions.

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          Most cited references16

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          MRBAYES: Bayesian inference of phylogenetic trees.

          The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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            Is a new and general theory of molecular systematics emerging?

            The advent and maturation of algorithms for estimating species trees-phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes-represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a "local optimum" for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term "phylogeny" for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.
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              Integrative taxonomy: a multisource approach to exploring biodiversity.

              Good alpha taxonomy is central to biology. On the basis of a survey of arthropod studies that used multiple disciplines for species delimitation, we evaluated the performance of single disciplines. All included disciplines had a considerable failure rate. Rigor in species delimitation can thus be increased when several disciplines chosen for complementarity are used. We present a flexible procedure and stopping rule for integrative taxonomy that uses the information from different disciplines separately. Disagreement among disciplines over the number and demarcation of species is resolved by elucidating and invoking evolutionary explanations for disagreement. With the identification of further promising study organisms and of new questions for in-depth analysis, evolutionary biology should profit from integrative taxonomy. An important rationale is clarity in researcher bias in the decision-making process. The success of integrative taxonomy will further increase through methodological progress, taxonomic training of evolutionary biologists, and balanced resource allocation.
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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
                10 December 2015
                2015
                : 10
                : 12
                : e0144544
                Affiliations
                [1 ]Department of Life Sciences, The Natural History Museum, London, United Kingdom
                [2 ]Department of General Biology and Ecology, Novosibirsk State University, Novosibirsk, Russia
                [3 ]Swedish Species Information Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
                [4 ]Entomological Department (Insectarium), The Moscow Zoo, Moscow, Russia
                [5 ]Norwegian Institute for Nature Research, Trondheim, Norway
                [6 ]Department of Bioscience, Aarhus University, Aarhus, Denmark
                [7 ]Gund Institute for Ecological Economics, University of Vermont, Burlington, Vermont, United States of America
                [8 ]Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
                [9 ]Royal Saskatchewan Museum, Regina, Saskatchewan, Canada
                SOUTHWEST UNIVERSITY, CHINA
                Author notes

                Competing Interests: The authors have the following interests: work in Greenland was supported by the Carlsberg Foundation (grants 2009-01-0534 and 2011-01-0463). There are no patents, products in development or marketed products to declare. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.

                Conceived and designed the experiments: PHW. Performed the experiments: PHW STW. Analyzed the data: PHW. Contributed reagents/materials/analysis tools: PHW AMB BC MVB FØ CR LLR JH CSS. Wrote the paper: PHW.

                Article
                PONE-D-15-26697
                10.1371/journal.pone.0144544
                4684343
                26657658
                4e5a3173-dd9f-41e8-aed7-019b1f1947f2
                © 2015 Williams 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
                : 18 June 2015
                : 19 November 2015
                Page count
                Figures: 9, Tables: 3, Pages: 26
                Funding
                The database of species’ distributions in Russia was created with the financial support from a Grant of the President of the Russian Federation for young Russian scientists (grant МК-6176.2015.4) (to AB). DNA barcodes for some of the material were funded by the Saskatchewan Ministry of Agriculture and the Canada-Saskatchewan Growing Forward 2 bi-lateral agreement (grant 20130112) (to CS). Work in Greenland was supported by the Carlsberg Foundation (grants 2009-01-0534 and 2011-01-0463) (to CR). DNA barcodes for some of the Norwegian material were funded by the Research Council of Norway (grant 266134/F50) and the Norwegian Biodiversity Information Centre (grant 70184209). The Norwegian part of the project was funded by the Taxonomy Initiative of the Norwegian Biodiversity Information Centre (grant 70184228) (to FO). DNA sequencing for some of the material was funded by the Agricultural Science and Technology Innovation Program, China (grant CAAS-ASTIP-2015-IAR) (to JH). Part of the database of species’ distributions in North America was created with financial support from grants from the National Science Foundation to John Ascher, Douglas Yanega, and Jerome Rozen (grants NSF-DBI 0956388 and NSF-DBI 0956340) (to LR). The funding agencies had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The other authors received no specific funding for this work.
                Categories
                Research Article
                Custom metadata
                All sequences are available from the online gene-sequence databases: GenBank ( ncbi.nlm.nih.gov/genbank/) and BOLD ( boldsystems.org). A detailed list of accession numbers for the sequence numbers deposited in these databases is given in the supporting information ( S2 File) in the manuscript.

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