401
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Botnen SS, Davey ML, Halvorsen R, Kauserud H. Sequence clustering threshold has little effect on the recovery of microbial community structure. Mol Ecol Resour 2018; 18:1064-1076. [PMID: 29673081 DOI: 10.1111/1755-0998.12894] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/21/2018] [Accepted: 04/11/2018] [Indexed: 11/27/2022]
Abstract
Analysis of microbial community structure by multivariate ordination methods, using data obtained by high-throughput sequencing of amplified markers (i.e., DNA metabarcoding), often requires clustering of DNA sequences into operational taxonomic units (OTUs). Parameters for the clustering procedure tend not to be justified but are set by tradition rather than being based on explicit knowledge. In this study, we explore the extent to which ordination results are affected by variation in parameter settings for the clustering procedure. Amplicon sequence data from nine microbial community studies, representing different sampling designs, spatial scales and ecosystems, were subjected to clustering into OTUs at seven different similarity thresholds (clustering thresholds) ranging from 87% to 99% sequence similarity. The 63 data sets thus obtained were subjected to parallel DCA and GNMDS ordinations. The resulting community structures were highly similar across all clustering thresholds. We explain this pattern by the existence of strong ecological structuring gradients and phylogenetically diverse sets of abundant OTUs that are highly stable across clustering thresholds. Removing low-abundance, rare OTUs had negligible effects on community patterns. Our results indicate that microbial data sets with a clear gradient structure are highly robust to choice of sequence clustering threshold.
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Affiliation(s)
- Synnøve Smebye Botnen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
- The University Centre in Svalbard, Longyearbyen, Norway
| | - Marie Louise Davey
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Rune Halvorsen
- Department of Research and Collections, Natural History Museum, University of Oslo, Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
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402
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Pei J, Chu C, Li X, Lu B, Wu Y. CLADES: A classification-based machine learning method for species delimitation from population genetic data. Mol Ecol Resour 2018; 18:1144-1156. [PMID: 29667323 DOI: 10.1111/1755-0998.12887] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 11/30/2022]
Abstract
Species are considered to be the basic unit of ecological and evolutionary studies. As multilocus genomic data are increasingly available, there have been considerable interests in the use of DNA sequence data to delimit species. In this study, we show that machine learning can be used for species delimitation. Our method treats the species delimitation problem as a classification problem for identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purposes. Each pair of known populations is combined to form training samples with a label of "same species" or "different species". We use support vector machine (SVM) to train a classifier using a set of summary statistics computed from training samples as features. The trained classifier can classify a test sample to two outcomes: "same species" or "different species". Given multilocus genomic data of multiple related organisms or populations, our method (called CLADES) performs species delimitation by first classifying pairs of populations. CLADES then delimits species by maximizing the likelihood of species assignment for multiple populations. CLADES is evaluated through extensive simulation and also tested on real genetic data. We show that CLADES is both accurate and efficient for species delimitation when compared with existing methods. CLADES can be useful especially when existing methods have difficulty in delimitation, for example with short species divergence time and gene flow.
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Affiliation(s)
- Jingwen Pei
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut
| | - Chong Chu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Xin Li
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut
| | - Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Yufeng Wu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut
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403
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Kuchta SR, Brown AD, Highton R. Disintegrating over space and time: Paraphyly and species delimitation in the Wehrle's Salamander complex. ZOOL SCR 2018. [DOI: 10.1111/zsc.12281] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Shawn R. Kuchta
- Department of Biological Sciences; Ohio Center for Ecology and Evolutionary Studies; Ohio University; Athens OH USA
| | - Ashley D. Brown
- Department of Biological Sciences; Ohio Center for Ecology and Evolutionary Studies; Ohio University; Athens OH USA
| | - Richard Highton
- Department of Biology; University of Maryland; College Park MD USA
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404
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Affiliation(s)
| | - Jesse M. Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX USA
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405
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Singhal S, Hoskin CJ, Couper P, Potter S, Moritz C. A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics. Syst Biol 2018; 67:1061-1075. [DOI: 10.1093/sysbio/syy026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/27/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University—Dominguez Hills, Carson, CA 90747, USA
| | - Conrad J Hoskin
- College of Science & Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Patrick Couper
- Biodiversity Program, Queensland Museum, South Brisbane, Queensland 4101, Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
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406
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Manzanilla V, Kool A, Nguyen Nhat L, Nong Van H, Le Thi Thu H, de Boer HJ. Phylogenomics and barcoding of Panax: toward the identification of ginseng species. BMC Evol Biol 2018; 18:44. [PMID: 29614961 PMCID: PMC5883351 DOI: 10.1186/s12862-018-1160-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 03/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. RESULTS We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. CONCLUSIONS MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.
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Affiliation(s)
- V Manzanilla
- The Natural History Museum, University of Oslo, Oslo, Norway.
| | - A Kool
- The Natural History Museum, University of Oslo, Oslo, Norway
| | - L Nguyen Nhat
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Nong Van
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Le Thi Thu
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H J de Boer
- The Natural History Museum, University of Oslo, Oslo, Norway
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407
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Schuster A, Cárdenas P, Pisera A, Pomponi SA, Kelly M, Wörheide G, Erpenbeck D. Seven new deep-water Tetractinellida (Porifera: Demospongiae) from the Galápagos Islands – morphological descriptions and DNA barcodes. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Astrid Schuster
- Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paco Cárdenas
- Department of Medicinal Chemistry, Division of Pharmacognosy, BioMedical Centre, Uppsala University, Uppsala, Sweden
| | - Andrzej Pisera
- Institute of Paleobiology, Polish Academy of Sciences, ul. Warszawa, Pol
| | - Shirley A Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft Pierce, FL, USA
| | - Michelle Kelly
- National Centre for Coasts and Oceans, National Institute of Water and Atmospheric Research, Auckland, New Zeal
| | - Gert Wörheide
- Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- SNSB – Bavarian State Collections of Palaeontology and Geology, Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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408
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Eilertsen MH, Georgieva MN, Kongsrud JA, Linse K, Wiklund H, Glover AG, Rapp HT. Genetic connectivity from the Arctic to the Antarctic: Sclerolinum contortum and Nicomache lokii (Annelida) are both widespread in reducing environments. Sci Rep 2018; 8:4810. [PMID: 29556042 PMCID: PMC5859262 DOI: 10.1038/s41598-018-23076-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/06/2018] [Indexed: 11/23/2022] Open
Abstract
The paradigm of large geographic ranges in the deep sea has been challenged by genetic studies, which often reveal putatively widespread species to be several taxa with more restricted ranges. Recently, a phylogeographic study revealed that the tubeworm Sclerolinum contortum (Siboglinidae) inhabits vents and seeps from the Arctic to the Antarctic. Here, we further test the conspecificity of the same populations of S. contortum with additional mitochondrial and nuclear markers. We also investigate the genetic connectivity of another species with putatively the same wide geographic range - Nicomache lokii (Maldanidae). Our results support the present range of S. contortum, and the range of N. lokii is extended from vents and seeps in the Nordic Seas to mud volcanoes in the Barbados Trench and Antarctic vents. Sclerolinum contortum shows more pronounced geographic structure than N. lokii, but whether this is due to different dispersal capacities or reflects the geographic isolation of the sampled localities is unclear. Two distinct mitochondrial lineages of N. lokii are present in the Antarctic, which may result from two independent colonization events. The environmental conditions inhabited by the two species and implications for their distinct habitat preference is discussed.
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Affiliation(s)
- Mari H Eilertsen
- Department of Biological Sciences, University of Bergen, PO Box 7800, N-5020, Bergen, Norway. .,K.G. Jebsen Centre for Deep-Sea Research, University of Bergen, PO Box 7803, N-5020, Bergen, Norway.
| | - Magdalena N Georgieva
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Jon A Kongsrud
- Department of Natural History, University Museum of Bergen, PO Box 7800, N-5020, Bergen, Norway
| | - Katrin Linse
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Helena Wiklund
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Adrian G Glover
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Hans T Rapp
- Department of Biological Sciences, University of Bergen, PO Box 7800, N-5020, Bergen, Norway.,K.G. Jebsen Centre for Deep-Sea Research, University of Bergen, PO Box 7803, N-5020, Bergen, Norway.,Uni Research, Uni Environment, PO Box 7810, N-5020, Bergen, Norway
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409
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Barley AJ, Brown JM, Thomson RC. Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent. Syst Biol 2018; 67:269-284. [PMID: 28945903 DOI: 10.1093/sysbio/syx073] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/31/2017] [Indexed: 11/14/2022] Open
Abstract
The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek to fill this gap by using simulation to characterize the sensitivity of inference under the multispecies coalescent (MSC) to several violations of model assumptions thought to be common in empirical data. We also assess the fit of the MSC model to empirical data in the context of species delimitation. Our results show substantial variation in model fit across data sets. Posterior predictive tests find the poorest model performance in data sets that were hypothesized to be impacted by model violations. We also show that while the inferences assuming the MSC are robust to minor model violations, such inferences can be biased under some biologically plausible scenarios. Taken together, these results suggest that researchers can identify individual data sets in which species delimitation under the MSC is likely to be problematic, thereby highlighting the cases where additional lines of evidence to identify species boundaries are particularly important to collect. Our study supports a growing body of work highlighting the importance of model checking in phylogenetics, and the usefulness of tailoring tests of model fit to assess the reliability of particular inferences. [Populations structure, gene flow, demographic changes, posterior prediction, simulation, genetics.].
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Affiliation(s)
- Anthony J Barley
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI 96822, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Robert C Thomson
- Department of Biology, University of Hawai'i, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI 96822, USA
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410
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Cadena CD, Zapata F, Jiménez I. Issues and Perspectives in Species Delimitation using Phenotypic Data: Atlantean Evolution in Darwin's Finches. Syst Biol 2018; 67:181-194. [PMID: 28945876 DOI: 10.1093/sysbio/syx071] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/30/2017] [Indexed: 11/13/2022] Open
Abstract
Progress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches employed in taxonomic studies using phenotypic data are often compromised by three issues: 1) reliance on graphical analyses that convey little information on phenotype frequencies; 2) exclusion of characters potentially important for species delimitation following reduction of data dimensionality; and 3) use of measures of central tendency to evaluate phenotypic distinctiveness. We outline approaches to overcome these issues based on statistical developments related to normal mixture models (NMMs) and illustrate them empirically with a reanalysis of morphological data recently used to claim that there are no morphologically distinct species of Darwin's ground-finches (Geospiza). We found negligible support for this claim relative to taxonomic hypotheses recognizing multiple species. Although species limits among ground-finches merit further assessments using additional sources of information, our results bear implications for other areas of inquiry including speciation research: because ground-finches have likely speciated and are not trapped in a process of "Sisyphean" evolution as recently argued, they remain useful models to understand the evolutionary forces involved in speciation. Our work underscores the importance of statistical approaches grounded on appropriate evolutionary models for species delimitation. We discuss how NMMs offer new perspectives in the kind of inferences available to systematists, with significant repercussions on ideas about the phenotypic structure of biodiversity.
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Affiliation(s)
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Iván Jiménez
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
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411
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Smith BT, Bryson RW, Mauck WM, Chaves J, Robbins MB, Aleixo A, Klicka J. Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae). Mol Phylogenet Evol 2018; 126:45-57. [PMID: 29551521 DOI: 10.1016/j.ympev.2018.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/31/2018] [Accepted: 03/09/2018] [Indexed: 01/05/2023]
Abstract
The New World avian family Polioptilidae (gnatcatchers and gnatwrens) is distributed from Argentina to Canada and includes 15 species and more than 60 subspecies. No study to date has evaluated phylogenetic relationships within this family and the historical pattern of diversification within the group remains unknown. Moreover, species limits, particularly in widespread taxa that show geographic variation, remain unclear. In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family. We then used the inferred diversity along with alternative taxonomic classification schemes to evaluate how lumping and splitting of both taxa and geographical areas influenced biogeographic inference. Species-tree analyses grouped Polioptilidae into four main clades: Microbates, Ramphocaenus, a Polioptila guianensis complex, and the remaining members of Polioptila. Ramphocaenus melanurus was sister to the clade containing M. cinereiventris and M. collaris, which formed a clade sister to all species within Polioptila. Polioptila was composed of two clades, the first of which included the P. guianensis complex; the other contained all remaining species in the genus. Using multispecies coalescent modeling, we inferred a more than 3-fold increase in species diversity, of which 87% represent currently recognized species or subspecies. Much of this diversity corresponded to subspecies that occur in the Neotropics. We identified three polyphyletic species, and delimited 4-6 previously undescribed candidate taxa. Probabilistic modeling of geographic ranges on the species tree indicated that the family likely had an ancestral origin in South America, with all three genera independently colonizing North America. Support for this hypothesis, however, was sensitive to the taxonomic classification scheme used and the number of geographical areas allowed. Our study proposes the first phylogenetic hypothesis for Polioptilidae and provides genealogical support for the reclassification of species limits. Species limits and the resolution of geographical areas that taxa inhabit influence the inferred spatial diversification history.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA; Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Robert W Bryson
- Burke Museum of Natural History and Culture and Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - William M Mauck
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Jaime Chaves
- Universidad San Francisco de Quito, Colegio de Ciencias Biológicas y Ambientales - Extensión Galápagos, Campus Cumbayá, Casilla Postal 17-1200-841, Quito, Ecuador
| | - Mark B Robbins
- University of Kansas Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Caixa Postal 399, CEP 66040-170 Belém, Brazil
| | - John Klicka
- Burke Museum of Natural History and Culture and Department of Biology, University of Washington, Seattle, WA 98195, USA
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412
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Roelke CE, Maldonado JA, Pope BW, Firneno TJ, Laduc TJ, Hibbitts TJ, Ryberg WA, Rains ND, Fujita MK. Mitochondrial genetic variation within and between Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis, the spot-tailed earless lizards of Texas. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1436726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Corey E. Roelke
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Jose A. Maldonado
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Blake W. Pope
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
| | - Thomas J. Firneno
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Travis J. Laduc
- Biodiversity Collections, Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Toby J. Hibbitts
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Wade A. Ryberg
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | | | - Matthew K. Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
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413
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Berriman JS, Ellingson RA, Awbrey JD, Rico DM, Valdés ÁA, Wilson NG, Aguilar A, Herbert DG, Hirano YM, Trowbridge CD, Krug PJ. A biting commentary: Integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume "killer algae". Mol Phylogenet Evol 2018. [PMID: 29524652 DOI: 10.1016/j.ympev.2018.02.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Predicting biotic resistance to highly invasive strains of "killer algae" (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe. Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae.
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Affiliation(s)
- John S Berriman
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Ryan A Ellingson
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Jaymes D Awbrey
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Diane M Rico
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Ángel A Valdés
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
| | - Nerida G Wilson
- Western Australian Museum, Kew Street, Welshpool, Perth, Western Australia 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Andres Aguilar
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - David G Herbert
- School of Life Sciences, University of KwaZulu-Natal, P. Bag X01, Scottsville 3209, South Africa
| | - Yayoi M Hirano
- Department of Biology, Graduate School of Science, Chiba University, Japan
| | - Cynthia D Trowbridge
- University of Oregon, Oregon Institute of Marine Biology, PO Box 5389, Charleston, OR 97420, USA
| | - Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA.
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414
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Zachos FE. Mammals and meaningful taxonomic units: the debate about species concepts and conservation. Mamm Rev 2018. [DOI: 10.1111/mam.12121] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Frank E. Zachos
- Natural History Museum Vienna; Mammal Collection; Burgring 7 1010 Vienna Austria
- Department of Integrative Zoology; University of Vienna; Althanstraße 14 1090 Vienna Austria
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415
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Noguerales V, Cordero PJ, Ortego J. Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers. Mol Ecol 2018; 27:1229-1244. [DOI: 10.1111/mec.14504] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/16/2017] [Accepted: 01/05/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ciudad Real Spain
| | - Pedro J. Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ciudad Real Spain
| | - Joaquín Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
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416
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Finding Evolutionary Processes Hidden in Cryptic Species. Trends Ecol Evol 2018; 33:153-163. [DOI: 10.1016/j.tree.2017.11.007] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/18/2022]
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417
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Resolving taxonomic turbulence and uncovering cryptic diversity in the musk turtles (Sternotherus) using robust demographic modeling. Mol Phylogenet Evol 2018; 120:1-15. [DOI: 10.1016/j.ympev.2017.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/09/2017] [Accepted: 11/16/2017] [Indexed: 01/25/2023]
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418
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Meik JM, Schaack S, Flores-Villela O, Streicher JW. Integrative taxonomy at the nexus of population divergence and speciation in insular speckled rattlesnakes. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1429689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Jesse M. Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, USA
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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419
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Reyes-Velasco J, Manthey JD, Bourgeois Y, Freilich X, Boissinot S. Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data. PLoS One 2018; 13:e0190440. [PMID: 29389966 PMCID: PMC5794058 DOI: 10.1371/journal.pone.0190440] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/14/2017] [Indexed: 11/18/2022] Open
Abstract
Understanding the diversification of biological lineages is central to evolutionary studies. To properly study the process of speciation, it is necessary to link micro-evolutionary studies with macro-evolutionary mechanisms. Micro-evolutionary studies require proper sampling across a taxon's range to adequately infer genetic diversity. Here we use the grass frogs of the genus Ptychadena from the Ethiopian highlands as a model to study the process of lineage diversification in this unique biodiversity hotspot. We used thousands of genome-wide SNPs obtained from double digest restriction site associated DNA sequencing (ddRAD-seq) in populations of the Ptychadena neumanni species complex from the Ethiopian highlands in order to infer their phylogenetic relationships and genetic structure, as well as to study their demographic history. Our genome-wide phylogenetic study supports the existence of approximately 13 lineages clustered into 3 species groups. Our phylogenetic and phylogeographic reconstructions suggest that those endemic lineages diversified in allopatry, and subsequently specialized to different habitats and elevations. Demographic analyses point to a continuous decrease in the population size across the majority of lineages and populations during the Pleistocene, which is consistent with a continuous period of aridification that East Africa experienced since the Pliocene. We discuss the taxonomic implications of our analyses and, in particular, we warn against the recent practice to solely use Bayesian species delimitation methods when proposing taxonomic changes.
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Affiliation(s)
| | - Joseph D. Manthey
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Yann Bourgeois
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Xenia Freilich
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States of America
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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420
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Voss RS, Díaz-Nieto JF, Jansa SA. A Revision ofPhilander(Marsupialia: Didelphidae), Part 1:P. quica,P. canus, and a New Species from Amazonia. AMERICAN MUSEUM NOVITATES 2018. [DOI: 10.1206/3891.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
| | - Juan F. Díaz-Nieto
- Departamento de Ciencias Biológicas and Grupo de Investigación BEC, Universidad EAFIT, Medellín, Colombia
| | - Sharon A. Jansa
- Department of Ecology, Evolution, and Behavior; and J.F. Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota
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421
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Thom G, Amaral FRD, Hickerson MJ, Aleixo A, Araujo-Silva LE, Ribas CC, Choueri E, Miyaki CY. Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species. Syst Biol 2018; 67:700-718. [DOI: 10.1093/sysbio/syy004] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/23/2018] [Indexed: 01/25/2023] Open
Affiliation(s)
- Gregory Thom
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Fabio Raposo Do Amaral
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP 09972–270, Brazil
| | - Michael J Hickerson
- Department of Biology, Marshak Science Building, City College of New York, 160, Convent Avenue, 10031 New York, NY, USA
| | - Alexandre Aleixo
- Departamento de Ornitologia, Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - Lucas E Araujo-Silva
- Departamento de Ornitologia, Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - Camila C Ribas
- Coordenação de biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, Brazil
| | - Erik Choueri
- Coordenação de biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, Brazil
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
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422
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Lörz AN, Tandberg AHS, Willassen E, Driskell A. Rhachotropis (Eusiroidea, Amphipoda) from the North East Atlantic. Zookeys 2018; 731:75-101. [PMID: 29472763 PMCID: PMC5810106 DOI: 10.3897/zookeys.731.19814] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/09/2017] [Indexed: 12/02/2022] Open
Abstract
The genus Rhachotropis has the widest geographic and bathymetric distribution of all amphipod genera worldwide. Molecular and morphological investigations of specimens sampled around Iceland and off the Norwegian coast allow the first insights into the relationships of North East Atlantic Rhachotropis. The 31 cytochrome oxidase subunit I (COI) sequences generated for this study were assigned 13 Barcode Index Numbers (BINs) in the Barcode of Life database (BOLD), of which 12 are new to the database. Molecular analyses of COI and 16S sequences could not confirm a theory that depth has a greater influence on the phylogeny of Rhachotropis than geographic distance. Although the North East Atlantic is a well-studied area, our molecular investigations revealed the genus Rhachotropis may contain cryptic species, which indicates a higher biodiversity than currently known. For example, the specimens which key to Rhachotropis helleri is a complex of three COI clades, two of which cannot be identified with morphological traits. One specimen of each of the clades in the cladogram was documented by high definition photographs. A special focus was on the visual morphology of the eyes, as this character shows interspecific differences within the genus Rhachotropis in response to fixation in ethanol. Detailed morphological investigation showed that some clades thought to be indistinguishable can be separated by minute but consistent morphological characters. Datamining Genbank to examine all registered COI-sequences of R. aculeata, the only previously known Rhachotropis BIN in the North Atlantic and sub-Arctic, showed R. aculeata to be subdivided by an Arctic and a North Atlantic population.
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Affiliation(s)
- Anne-Nina Lörz
- University of Hamburg, CeNak, Centre of Natural History, Zoological Museum, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Anne Helene S. Tandberg
- University of Bergen, University Museum, Department of Natural History, PO Box 7800, 5020 Bergen, Norway
| | - Endre Willassen
- University of Bergen, University Museum, Department of Natural History, PO Box 7800, 5020 Bergen, Norway
| | - Amy Driskell
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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423
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Vidigal THDA, Coscarelli D, Paixão H, Bernardes S, Montresor LC, Pepato AR. Integrative taxonomy of the neotropical genusOmalonyx(Elasmognatha: Succineidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Daniel Coscarelli
- Departamento de Zoologia; Universidade Federal de Minas Gerais; Belo Horizonte Brazil
| | - Hugo Paixão
- Departamento de Zoologia; Universidade Federal de Minas Gerais; Belo Horizonte Brazil
| | - Samuel Bernardes
- Departamento de Zoologia; Universidade Federal de Minas Gerais; Belo Horizonte Brazil
| | - Lângia C. Montresor
- Laboratório de Malacologia; Instituto Oswaldo Cruz; Fundação Oswaldo Cruz; Rio de Janeiro Brazil
| | - Almir R. Pepato
- Departamento de Zoologia; Universidade Federal de Minas Gerais; Belo Horizonte Brazil
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424
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Gale SW, Duangjai S, Li J, Ito Y, Watthana S, Termwutthipreecha P, Cheuk ML, Suddee S. Integrative analyses of Nervilia (Orchidaceae) section Linervia reveal further undescribed cryptic diversity in Thailand. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2017.1415233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Stephan W. Gale
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Sutee Duangjai
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Jihong Li
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Yu Ito
- Plant Phylogenetics and Conservation Group, Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Santi Watthana
- School of Biology, Institute of Science, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima 30000, Thailand
| | - Phatsara Termwutthipreecha
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Mang Lung Cheuk
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Somran Suddee
- Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok 10900, Thailand
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425
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Musher LJ, Cracraft J. Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus). Mol Phylogenet Evol 2018; 118:204-221. [DOI: 10.1016/j.ympev.2017.09.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/16/2017] [Accepted: 09/18/2017] [Indexed: 11/24/2022]
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426
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Eldridge RA, Achmadi AS, Giarla TC, Rowe KC, Esselstyn JA. Geographic isolation and elevational gradients promote diversification in an endemic shrew on Sulawesi. Mol Phylogenet Evol 2018; 118:306-317. [DOI: 10.1016/j.ympev.2017.09.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 08/08/2017] [Accepted: 09/25/2017] [Indexed: 01/06/2023]
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427
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O'Connell KA, Smith EN, Shaney KJ, Arifin U, Kurniawan N, Sidik I, Fujita MK. Coalescent species delimitation of a Sumatran parachuting frog. ZOOL SCR 2017. [DOI: 10.1111/zsc.12248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kyle A O'Connell
- Department of Biology The University of Texas at Arlington Arlington TX USA
- The Amphibian and Reptile Diversity Research Center University of Texas at Arlington Arlington TX USA
| | - Eric N Smith
- Department of Biology The University of Texas at Arlington Arlington TX USA
- The Amphibian and Reptile Diversity Research Center University of Texas at Arlington Arlington TX USA
| | - Kyle J Shaney
- Department of Biology The University of Texas at Arlington Arlington TX USA
- The Amphibian and Reptile Diversity Research Center University of Texas at Arlington Arlington TX USA
| | - Umilaela Arifin
- Biozentrum Grindel & Zopolofisches Museum Universität Hamburg Hamburg Germany
| | - Nia Kurniawan
- Department of Biology Universitas Brawijaya Malang East Java Indonesia
| | - Irvan Sidik
- Research and Development Center for Biology Indonesian Institute of Science (LIPI) Cibinong West Java Indonesia
| | - Matthew K Fujita
- Department of Biology The University of Texas at Arlington Arlington TX USA
- The Amphibian and Reptile Diversity Research Center University of Texas at Arlington Arlington TX USA
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428
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Suárez-Villota EY, Carmignotto AP, Brandão MV, Percequillo AR, Silva MJDJ. Systematics of the genus Oecomys (Sigmodontinae: Oryzomyini): molecular phylogenetic, cytogenetic and morphological approaches reveal cryptic species. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx095] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elkin Y Suárez-Villota
- Laboratório de Ecologia e Evolução, Instituto Butantan, Av. Vital Brazil, São Paulo, Brazil
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Edificio Emilio Pugín, campus Isla Teja, Valdivia, Chile
| | - Ana Paula Carmignotto
- Laboratório de Diversidade Animal, Departamento de Biologia, Universidade Federal de São Carlos, campus Sorocaba, Rodovia João Leme dos Santos, Sorocaba, São Paulo, Brazil
| | - Marcus Vinícius Brandão
- Laboratório de Diversidade Animal, Departamento de Biologia, Universidade Federal de São Carlos, campus Sorocaba, Rodovia João Leme dos Santos, Sorocaba, São Paulo, Brazil
| | - Alexandre Reis Percequillo
- Departamento de Ciências Biolόgicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Av. Pádua Dias, Piracicaba, São Paulo, Brazil
| | - Maria José de J Silva
- Laboratório de Ecologia e Evolução, Instituto Butantan, Av. Vital Brazil, São Paulo, Brazil
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429
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Sproul JS, Maddison DR. Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- John S Sproul
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - David R Maddison
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
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430
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Martinsson S, Erséus C. Cryptic diversity in supposedly species-poor genera of Enchytraeidae (Annelida: Clitellata). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Svante Martinsson
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
| | - Christer Erséus
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
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431
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Abstract
Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus.IMPORTANCE The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.
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432
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Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon. Mol Phylogenet Evol 2017; 117:10-29. [DOI: 10.1016/j.ympev.2017.08.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 02/06/2023]
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433
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Carbayo F, Silva MS, Riutort M, Álvarez-Presas M. Rolling into the deep of the land planarian genus Choeradoplana (Tricladida, Continenticola, Geoplanidae) taxonomy. ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-017-0352-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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434
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Segatto ALA, Reck-Kortmann M, Turchetto C, Freitas LB. Multiple markers, niche modelling, and bioregions analyses to evaluate the genetic diversity of a plant species complex. BMC Evol Biol 2017; 17:234. [PMID: 29187208 PMCID: PMC5707870 DOI: 10.1186/s12862-017-1084-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/17/2017] [Indexed: 02/01/2023] Open
Abstract
Background The classification of closely related plants is not straightforward. These morphologically similar taxa frequently maintain their inter-hybridization potential and share ancestral polymorphisms as a consequence of their recent divergence. Under the biological species concept, they may thus not be considered separate species. The Petunia integrifolia complex is especially interesting because, in addition to the features mentioned above, its taxa share a pollinator, and their geographical ranges show multiple overlaps. Here, we combined plastid genome sequences, nuclear microsatellites, AFLP markers, ecological niche modelling, and bioregions analysis to investigate the genetic variability between the different taxa of the P. integrifolia complex in a comprehensive sample covering the entire geographical range of the complex. Results Results from molecular markers did not fully align with the current taxonomic classification. Niche modelling and bioregions analyses revealed that taxa were associated with different ecological constraints, indicating that the habitat plays an important role in preserving species boundaries. For three taxa, our analyses showed a mostly conserved, non-overlapping geographical distribution over time. However, for two taxa, niche modelling found an overlapping distribution over time; these taxa were also associated with the same bioregions. Conclusions cpDNA markers were better able to discriminate between Petunia taxa than SSRs and AFLPs. Overall, our results suggest that the P. integrifolia complex represents a continuum of individuals from distant and historically isolated populations, which share some morphological traits, but are established in four different evolutionary lineages. Electronic supplementary material The online version of this article (10.1186/s12862-017-1084-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Lúcia A Segatto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Porto Alegre, RS, 91501-970, Brazil
| | - Maikel Reck-Kortmann
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Porto Alegre, RS, 91501-970, Brazil
| | - Caroline Turchetto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Porto Alegre, RS, 91501-970, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Porto Alegre, RS, 91501-970, Brazil.
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435
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Yu G, Rao D, Matsui M, Yang J. Coalescent-based delimitation outperforms distance-based methods for delineating less divergent species: the case of Kurixalus odontotarsus species group. Sci Rep 2017; 7:16124. [PMID: 29170403 PMCID: PMC5700917 DOI: 10.1038/s41598-017-16309-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 11/10/2017] [Indexed: 12/30/2022] Open
Abstract
Few empirical studies have compared coalescent-based methods to distance-based methods for delimitation of less divergent species. In this study, we used two coalescent-based (BFD and BPP) and two distance-based barcoding (ABGD and jMOTU) methods to delimit closely related species in the Kurixalus odontotarsus species group. Phylogenetic analyses revealed that the K. odontotarsus species group comprises 11 distinct maternal clades with strong support values. Based on the genetic and morphological evidences, we consider that species diversity in the K. odontotarsus species group was underestimated and the 11 clades represent 11 species, of which six are unnamed. The coalescent-based delimitations decisively supported the scenario of 11-species corresponding to the 11 clades. However, the distance-based ABGD only obtained 3-6 candidate species, which is not consistent with morphological evidence. These results indicate that BFD and BPP are more conservative than ABGD to false negatives (lumping). Method of fixed threshold (jMOTU) may obtain a resolution similar to that inferred by BFD and BPP, but it severely relies on subjective choice of the threshold and lacks statistical support. We consider that coalescent-based BFD and BPP approaches outperform distance-based methods for delineation of less divergent species.
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Affiliation(s)
- Guohua Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China
| | - Dingqi Rao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Kakyo-ku, Kyoto, 606-8501, Japan
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China.
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436
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Gaubert P, Antunes A, Meng H, Miao L, Peigné S, Justy F, Njiokou F, Dufour S, Danquah E, Alahakoon J, Verheyen E, Stanley WT, O’Brien SJ, Johnson WE, Luo SJ. The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth. J Hered 2017; 109:347-359. [DOI: 10.1093/jhered/esx097] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l’Evolution de Montpellier (ISEM)—UM-CNRS-IRD-EPHE, Université, France
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
| | - Hao Meng
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
| | - Lin Miao
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
| | - Stéphane Peigné
- Centre de recherche sur la paléobiodiversité et les paléoenvironnements (CR2P)—UMR 7207 MNHN/CNRS/UPMC, Muséum national d’Histoire naturelle—CP38, France
| | - Fabienne Justy
- Institut des Sciences de l’Evolution de Montpellier (ISEM)—UM-CNRS-IRD-EPHE, Université, France
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Université de Yaoundé I, Faculté des Sciences, Cameroon
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Ghana
| | | | - Erik Verheyen
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Belgium
- Evolutionary Ecology Group, University of Antwerp, Belgium
| | | | - Stephen J O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
- Oceanographic Center, Dania Beach, FL
- Nova Southeastern University, Ft Lauderdale, FL
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA
| | - Shu-Jin Luo
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
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437
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Dornburg A, Townsend JP, Wang Z. Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. ADVANCES IN GENETICS 2017; 100:1-47. [PMID: 29153398 DOI: 10.1016/bs.adgen.2017.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.
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Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, United States
| | | | - Zheng Wang
- Yale University, New Haven, CT, United States.
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438
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Oxelman B, Brysting AK, Jones GR, Marcussen T, Oberprieler C, Pfeil BE. Phylogenetics of Allopolyploids. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017. [DOI: 10.1146/annurev-ecolsys-110316-022729] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Department of Biology and Environmental Sciences, University of Gothenburg, SE405 30 Göteborg, Sweden
| | - Anne Krag Brysting
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Graham R. Jones
- Gothenburg Global Biodiversity Centre, Department of Biology and Environmental Sciences, University of Gothenburg, SE405 30 Göteborg, Sweden
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, D-93053 Regensburg, Germany
| | - Bernard E. Pfeil
- Gothenburg Global Biodiversity Centre, Department of Biology and Environmental Sciences, University of Gothenburg, SE405 30 Göteborg, Sweden
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439
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Eilertsen MH, Kongsrud JA, Alvestad T, Stiller J, Rouse GW, Rapp HT. Do ampharetids take sedimented steps between vents and seeps? Phylogeny and habitat-use of Ampharetidae (Annelida, Terebelliformia) in chemosynthesis-based ecosystems. BMC Evol Biol 2017; 17:222. [PMID: 29089027 PMCID: PMC5664827 DOI: 10.1186/s12862-017-1065-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/15/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A range of higher animal taxa are shared across various chemosynthesis-based ecosystems (CBEs), which demonstrates the evolutionary link between these habitats, but on a global scale the number of species inhabiting multiple CBEs is low. The factors shaping the distributions and habitat specificity of animals within CBEs are poorly understood, but geographic proximity of habitats, depth and substratum have been suggested as important. Biogeographic studies have indicated that intermediate habitats such as sedimented vents play an important part in the diversification of taxa within CBEs, but this has not been assessed in a phylogenetic framework. Ampharetid annelids are one of the most commonly encountered animal groups in CBEs, making them a good model taxon to study the evolution of habitat use in heterotrophic animals. Here we present a review of the habitat use of ampharetid species in CBEs, and a multi-gene phylogeny of Ampharetidae, with increased taxon sampling compared to previous studies. RESULTS The review of microhabitats showed that many ampharetid species have a wide niche in terms of temperature and substratum. Depth may be limiting some species to a certain habitat, and trophic ecology and/or competition are identified as other potentially relevant factors. The phylogeny revealed that ampharetids have adapted into CBEs at least four times independently, with subsequent diversification, and shifts between ecosystems have happened in each of these clades. Evolutionary transitions are found to occur both from seep to vent and vent to seep, and the results indicate a role of sedimented vents in the transition between bare-rock vents and seeps. CONCLUSION The high number of ampharetid species recently described from CBEs, and the putative new species included in the present phylogeny, indicates that there is considerable diversity still to be discovered. This study provides a molecular framework for future studies to build upon and identifies some ecological and evolutionary hypotheses to be tested as new data is produced.
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Affiliation(s)
- Mari H Eilertsen
- Department of Biology, University of Bergen, Bergen, Norway.
- K.G. Jebsen Centre for Deep-Sea Research, University of Bergen, Bergen, Norway.
| | - Jon A Kongsrud
- Department of Natural History, University Museum of Bergen, Bergen, Norway
| | - Tom Alvestad
- Department of Natural History, University Museum of Bergen, Bergen, Norway
| | - Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, California, USA
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, California, USA
| | - Hans T Rapp
- Department of Biology, University of Bergen, Bergen, Norway
- K.G. Jebsen Centre for Deep-Sea Research, University of Bergen, Bergen, Norway
- Uni Research, Uni Environment, Bergen, Norway
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440
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Smith CH, Johnson NA, Pfeiffer JM, Gangloff MM. Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus). Mol Phylogenet Evol 2017; 119:50-62. [PMID: 29074460 DOI: 10.1016/j.ympev.2017.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 10/20/2017] [Accepted: 10/22/2017] [Indexed: 11/19/2022]
Abstract
Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent 'Strophitus' connasaugaensis and 'Strophitus' subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize the potential for a third putative species (Strophitus sp. cf. pascagoulaensis). Our findings aid stakeholders in establishing conservation and management strategies for the members of Anodontoides, Strophitus, and Pseudodontoideus.
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Affiliation(s)
- Chase H Smith
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL 32653, USA
| | - Nathan A Johnson
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - John M Pfeiffer
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Michael M Gangloff
- Biology Department, Appalachian State University, Boone, NC 28608-2027, USA
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441
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Laver RJ, Nielsen SV, Rosauer DF, Oliver PM. Trans-biome diversity in Australian grass-specialist lizards (Diplodactylidae: Strophurus). Mol Phylogenet Evol 2017; 115:62-70. [DOI: 10.1016/j.ympev.2017.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 05/30/2017] [Accepted: 07/13/2017] [Indexed: 11/27/2022]
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442
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Chan KO, Alexander AM, Grismer LL, Su YC, Grismer JL, Quah ESH, Brown RM. Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs. Mol Ecol 2017; 26:5435-5450. [DOI: 10.1111/mec.14296] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Kin Onn Chan
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - Alana M. Alexander
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology; Kaohsiung Medical University; Kaohsiung City Taiwan
| | - Jesse L. Grismer
- Department of Biological Sciences; Auburn University; Auburn AL USA
- La Kretz Center for Californian Conservation Science; Institute of the Environment and Sustainability; University of California Los Angeles; Los Angeles CA USA
| | - Evan S. H. Quah
- School of Biological Sciences; Universiti Sains Malaysia; Penang Malaysia
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
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443
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Turissini DA, Gomez OM, Teixeira MM, McEwen JG, Matute DR. Species boundaries in the human pathogen Paracoccidioides. Fungal Genet Biol 2017; 106:9-25. [PMID: 28602831 PMCID: PMC8335726 DOI: 10.1016/j.fgb.2017.05.007] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/12/2017] [Accepted: 05/31/2017] [Indexed: 12/29/2022]
Abstract
The use of molecular taxonomy for identifying recently diverged species has transformed the study of speciation in fungi. The pathogenic fungus Paracoccidioides spp has been hypothesized to be composed of five phylogenetic species, four of which compose the brasiliensis species complex. Nuclear gene genealogies support this divergence scenario, but mitochondrial loci do not; while all species from the brasiliensis complex are differentiated at nuclear coding loci, they are not at mitochondrial loci. We addressed the source of this incongruity using 11 previously published gene fragments, 10 newly-sequenced nuclear non-coding loci, and 10 microsatellites. We hypothesized and further demonstrated that the mito-nuclear incongruence in the brasiliensis species complex results from interspecific hybridization and mitochondrial introgression, a common phenomenon in eukaryotes. Additional population genetic analyses revealed possible nuclear introgression but much less than that seen in the mitochondrion. Our results are consistent with a divergence scenario of secondary contact and subsequent mitochondrial introgression despite the continued persistence of species boundaries. We also suggest that yeast morphology slightly-but significantly-differs across all five Paracoccidioides species and propose to elevate four of these phylogenetic species to formally described taxonomic species.
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Affiliation(s)
- David A Turissini
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Oscar M Gomez
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia; Biology Institute, Universidad de Antioquia, Medellín, Colombia
| | - Marcus M Teixeira
- Northern Arizona Center for Valley Fever Research, Flagstaff, AZ, USA
| | - Juan G McEwen
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA.
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444
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Larsen BB, Miller EC, Rhodes MK, Wiens JJ. Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life. QUARTERLY REVIEW OF BIOLOGY 2017. [DOI: 10.1086/693564] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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445
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Afonso Silva AC, Santos N, Ogilvie HA, Moritz C. Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology. PeerJ 2017; 5:e3724. [PMID: 28875076 PMCID: PMC5580384 DOI: 10.7717/peerj.3724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography, in an integrative taxonomy framework. Deep phylogeographic divergences have been reported for several species of Carlia skinks, but only for some eastern taxa have species boundaries been formally tested. The present study does this and revises the taxonomy for two species from northern Australia, Carlia johnstonei and C. triacantha. We introduce an approach that is based on the recently published method StarBEAST2, which uses multilocus data to explore the support for alternative species delimitation hypotheses using Bayes Factors (BFD). We apply this method, jointly with two other multispecies coalescent methods, using an extensive (from 2,163 exons) data set along with measures of 11 morphological characters. We use this integrated approach to evaluate two new candidate species previously revealed in phylogeographic analyses of rainbow skinks (genus Carlia) in Western Australia. The results based on BFD StarBEAST2, BFD* SNAPP and BPP genetic delimitation, together with morphology, support each of the four recently identified Carlia lineages as separate species. The BFD StarBEAST2 approach yielded results highly congruent with those from BFD* SNAPP and BPP. This supports use of the robust multilocus multispecies coalescent StarBEAST2 method for species delimitation, which does not require a priori resolved species or gene trees. Compared to the situation in C. triacantha, morphological divergence was greater between the two lineages within Kimberley endemic C. johnstonei, which also had deeper divergent histories. This congruence supports recognition of two species within C. johnstonei. Nevertheless, the combined evidence also supports recognition of two taxa within the more widespread C. triacantha. With this work, we describe two new species, Carlia insularis sp. nov and Carlia isostriacantha sp. nov. in the northwest of Australia. This contributes to increasing recognition that this region of tropical Australia has a rich and unique fauna.
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Affiliation(s)
- Ana C. Afonso Silva
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Natali Santos
- Universidade Federal do ABC, Santo André, SP, Brazil
| | - Huw A. Ogilvie
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
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446
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Bernardes SC, Pepato AR, von Rintelen T, von Rintelen K, Page TJ, Freitag H, de Bruyn M. The complex evolutionary history and phylogeography of Caridina typus (Crustacea: Decapoda): long-distance dispersal and cryptic allopatric species. Sci Rep 2017; 7:9044. [PMID: 28831142 PMCID: PMC5567278 DOI: 10.1038/s41598-017-08494-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/30/2017] [Indexed: 11/09/2022] Open
Abstract
The evolutionary history of the old, diverse freshwater shrimp genus Caridina is still poorly understood, despite its vast distribution – from Africa to Polynesia. Here, we used nuclear and mitochondrial DNA to infer the phylogeographic and evolutionary history of C. typus, which is one of only four species distributed across the entire range of the genus. Despite this species’ potential for high levels of gene flow, questions have been raised regarding its phylogeographic structure and taxonomic status. We identified three distinct lineages that likely diverged in the Miocene. Molecular dating and ancestral range reconstructions are congruent with C. typus’ early dispersal to Africa, possibly mediated by the Miocene Indian Ocean Equatorial Jet, followed by back dispersal to Australasia after the Jet’s closure. Furthermore, several different species delimitation methods indicate each lineage represents a distinct (cryptic) species, contradicting current morphospecies delimitation of a single C. typus taxon. The evolutionary history of C. typus lineages is complex, in which ancient oceanic current systems and (currently unrecognised) speciation events preceded secondary sympatry of these cryptic species.
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Affiliation(s)
- Samuel C Bernardes
- Laboratório de Acarologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, 31270-901, Brazil.
| | - Almir R Pepato
- Laboratório de Acarologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, 31270-901, Brazil
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin, 10115, Germany
| | - Kristina von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin, 10115, Germany
| | - Timothy J Page
- Australian Rivers Institute, Griffith University, Nathan, Queensland 4111, Australia.,Water Planning Ecology, Queensland Department of Science, Information Technology and Innovation, Dutton Park, Queensland 4102, Australia
| | - Hendrik Freitag
- Department of Biology, School of Science & Engineering, Ateneo de Manila University, Quezon City, 1108, Philippines
| | - Mark de Bruyn
- School of Biological Sciences, Bangor University, Bangor, LL57 2UW, UK. .,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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447
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Kindler C, Chèvre M, Ursenbacher S, Böhme W, Hille A, Jablonski D, Vamberger M, Fritz U. Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species. Sci Rep 2017; 7:7378. [PMID: 28785033 PMCID: PMC5547120 DOI: 10.1038/s41598-017-07847-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/03/2017] [Indexed: 11/09/2022] Open
Abstract
Recent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes and identified previously unknown secondary contact zones. Until now, little is known about gene flow across these contact zones. Using two mitochondrial markers and 13 microsatellite loci, we examined two contact zones. One, largely corresponding to the Rhine region, involves the western subspecies Natrix natrix helvetica and the eastern subspecies N. n. natrix, whereas in the other, more easterly, contact zone two lineages meet that are currently identified with N. n. natrix and N. n. persa. This second contact zone runs across Central Europe to the southern Balkans. Our analyses reveal that the western contact zone is narrow, with parapatrically distributed mitochondrial lineages and limited, largely unidirectional nuclear gene flow. In contrast, the eastern contact zone is very wide, with massive nuclear admixture and broadly overlapping mitochondrial lineages. In combination with additional lines of evidence (morphology, phylogeny, divergence times), we conclude that these differences reflect different stages in the speciation process and that Natrix helvetica should be regarded as a distinct species. We suggest a nomenclatural framework for presently recognized grass snake taxa and highlight the need for reconciling the conflicts between genetics and taxonomy.
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Affiliation(s)
- Carolin Kindler
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Maxime Chèvre
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, 4056, Basel, Switzerland
| | - Sylvain Ursenbacher
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, 4056, Basel, Switzerland.,Karch, Passage Maximilien-de-Meuron 6, 2000, Neuchâtel, Switzerland
| | - Wolfgang Böhme
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Axel Hille
- Rosengarten 21, 33605, Bielefeld, Germany
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Melita Vamberger
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany.
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448
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Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties. Heredity (Edinb) 2017; 119:287-294. [PMID: 28767104 DOI: 10.1038/hdy.2017.46] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 12/12/2022] Open
Abstract
Past shifts in connectivity in riverine environments (for example, sea-level changes) and the properties of current drainages can act as drivers of genetic structure and demographic processes in riverine population of fishes. However, it is unclear whether the same river properties that structure variation on recent timescales will also leave similar genomic signatures that reflect paleodrainage properties. By characterizing genetic structure in a freshwater fish species (Hollandichthys multifasciatus) from a system of basins along the Atlantic coast of Brazil we test for the effects of paleodrainages caused by sea-level changes during the Pleistocene. Given that the paleodrainage properties differ along the Brazilian coast, we also evaluate whether estimated genetic diversity within paleodrainages can be explained by past riverine properties (i.e., area and number of rivers in a paleodrainage). Our results demonstrate that genetic structure between populations is not just highly concordant with paleodrainages, but that differences in the genetic diversity among paleodrainages correspond to the joint effect of differences in the area encompassed by, and the number of rivers, within a paleodrainage. Our findings extend the influence of current riverine properties on genetic diversity to those associated with past paleodrainage properties. We discuss how these findings may explain the inconsistent support for paleodrainages in structuring divergence from different global regions and the importance of taking into account past conditions for understanding the high species diversity of freshwater fish that we currently observe in the world, and especially in the Neotropics.
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449
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Malaney JL, Demboski JR, Cook JA. Integrative species delimitation of the widespread North American jumping mice (Zapodinae). Mol Phylogenet Evol 2017; 114:137-152. [PMID: 28600183 DOI: 10.1016/j.ympev.2017.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/12/2017] [Accepted: 06/01/2017] [Indexed: 01/10/2023]
Abstract
Delimiting species can be challenging, but is a key step for the critical examination of evolutionary history and for prioritizing conservation efforts. Because systematic relationships are often determined iteratively using tests based on taxonomy, such methods can fail to detect cryptic variation and result in biased conclusions. Conversely, discovery-based approaches provide a powerful way to define operational taxonomic units and test species boundaries. We compare both approaches (taxonomy-based delimitation - TBD and discovery-based delimitation - DBD) within North American jumping mice (Zapodinae) using broad sampling, multilocus analyses, and ecological tests. This group diversified through the dynamic glacial-interglacial periods of the Quaternary and phylogeographic tests reveal 28 lineages that correspond poorly with current taxonomy (4 species, 32 nominal subspecies). However, neither the 4-species or 28-lineage hypotheses are optimal for species-level classification. Rather, information theoretic approaches (Bayes Factors) indicate a 15-species hypothesis is best for characterizing genetic variation in this group, with subsequent iterative pairwise ecological tests failing to confirm four species pairs. Taken together, evolutionary and ecological tests capture divergence among 11 putative species that, if upheld by additional tests, will lead to taxonomic revision and reevaluation of conservation plans.
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Affiliation(s)
- Jason L Malaney
- Department of Biology, Austin Peay State University, Clarksville, TN 37044, USA; Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA.
| | - Joseph A Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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450
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Laurent RAS, Herbin D, Mielke CGC. Revision of the genus Reinmara Schaus, 1928 (Lepidoptera, Mimallonoidea, Mimallonidae) with the descriptions of four new species from South America. Zookeys 2017:97-129. [PMID: 28769690 PMCID: PMC5534525 DOI: 10.3897/zookeys.677.12435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 04/26/2017] [Indexed: 11/12/2022] Open
Abstract
The mimallonid genus Reinmara Schaus, 1928 is revised. The three previously described species, R. enthona (Schaus, 1905), R. minasa Schaus, 1928, and R. wolfei Herbin & C. Mielke, 2014 are redescribed and the females of each are described and figured for the first time. Additionally, we describe four new species, two Andean: R. andensissp. n. and R. occidentalissp. n., and two Brazilian: R. atlanticasp. n. and R. igneasp. n.. The new species R. ignea and R. atlantica are likely of conservation concern due to their rarity in collections and their apparent endemism to an endangered biome, the Brazilian Atlantic Forest.
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Affiliation(s)
- Ryan A St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611-2710 USA
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