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Monjaraz-Ruedas R, Prendini L, Francke OF. Systematics of the Short-Tailed Whipscorpion Genus Stenochrus Chamberlin, 1922 (Schizomida: Hubbardiidae), with Descriptions of Six New Genera and Five New Species. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2019. [DOI: 10.1206/0003-0090.435.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Rodrigo Monjaraz-Ruedas
- Posgrado en Ciencias Biológicas. Universidad Nacional Autónoma de México; Colección Nacional de Arácnidos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México
| | - Lorenzo Prendini
- Division of Invertebrate Zoology. American Museum of Natural History
| | - Oscar F. Francke
- Colección Nacional de Arácnidos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México
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2
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Lin SW, Lopardo L, Haase M, Uhl G. Taxonomic revision of the dwarf spider genus Shaanxinus Tanasevitch, 2006 (Araneae, Linyphiidae, Erigoninae), with new species from Taiwan and Vietnam. ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-018-00389-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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3
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Billet G, Bardin J. Serial Homology and Correlated Characters in Morphological Phylogenetics: Modeling the Evolution of Dental Crests in Placentals. Syst Biol 2018; 68:267-280. [DOI: 10.1093/sysbio/syy071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/22/2018] [Indexed: 01/24/2023] Open
Affiliation(s)
- Guillaume Billet
- CR2P, UMR 7207, Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, 8 rue Buffon 75005 Paris, France
| | - Jérémie Bardin
- CR2P, UMR 7207, Sorbonne Université, MNHN, CNRS, T.46-56, E.5, case 104, 4 place Jussieu, 75252 Paris cedex 05, France
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4
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Elgorriaga A, Escapa IH, Rothwell GW, Tomescu AMF, Rubén Cúneo N. Origin of Equisetum: Evolution of horsetails (Equisetales) within the major euphyllophyte clade Sphenopsida. AMERICAN JOURNAL OF BOTANY 2018; 105:1286-1303. [PMID: 30025163 DOI: 10.1002/ajb2.1125] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Equisetum is the sole living representative of Sphenopsida, a clade with impressive species richness, a long fossil history dating back to the Devonian, and obscure relationships with other living pteridophytes. Based on molecular data, the crown group age of Equisetum is mid-Paleogene, although fossils with possible crown synapomorphies appear in the Triassic. The most widely circulated hypothesis states that the lineage of Equisetum derives from calamitaceans, but no comprehensive phylogenetic studies support the claim. Using a combined approach, we provide a comprehensive phylogenetic analysis of Equisetales, with special emphasis on the origin of genus Equisetum. METHODS We performed parsimony phylogenetic analyses to address relationships of 43 equisetalean species (15 extant, 28 extinct) using a combination of morphological and molecular characters. KEY RESULTS We recovered Equisetaceae + Neocalamites as sister to Calamitaceae + a clade of Angaran and Gondwanan horsetails, with the four groups forming a clade that is sister to Archaeocalamitaceae. The estimated age for the Equisetum crown group is mid-Mesozoic. CONCLUSIONS Modern horsetails are not nested within calamitaceans; instead, both groups have explored independent evolutionary trajectories since the Carboniferous. Diverse fossil taxon sampling helps to shed light on the position and relationships of equisetalean lineages, of which only a tiny remnant is present within the extant flora. Understanding these relationships and early character configurations of ancient plant clades as Equisetales provide useful tests of hypotheses about overall phylogenetic relationships of euphyllophytes and foundations for future tests of molecular dates with paleontological data.
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Affiliation(s)
- Andrés Elgorriaga
- CONICET, Museo Paleontológico Egidio Feruglio, Trelew, Chubut, 9100, Argentina
| | - Ignacio H Escapa
- CONICET, Museo Paleontológico Egidio Feruglio, Trelew, Chubut, 9100, Argentina
| | - Gar W Rothwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - Alexandru M F Tomescu
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - N Rubén Cúneo
- CONICET, Museo Paleontológico Egidio Feruglio, Trelew, Chubut, 9100, Argentina
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Abstract
It is time to escape the constraints of the Systematics Wars narrative and pursue new questions that are better positioned to establish the relevance of the field in this time period to broader issues in the history of biology and history of science. To date, the underlying assumptions of the Systematics Wars narrative have led historians to prioritize theory over practice and the conflicts of a few leading theorists over the less-polarized interactions of systematists at large. We show how shifting to a practice-oriented view of methodology, centered on the trajectory of mathematization in systematics, demonstrates problems with the common view that one camp (cladistics) straightforwardly "won" over the other (phenetics). In particular, we critique David Hull's historical account in Science as a Process by demonstrating exactly the sort of intermediate level of positive sharing between phenetic and cladistic theories that undermines their mutually exclusive individuality as conceptual systems over time. It is misleading, or at least inadequate, to treat them simply as holistically opposed theories that can only interact by competition to the death. Looking to the future, we suggest that the concept of workflow provides an important new perspective on the history of mathematization and computerization in biology after World War II.
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Affiliation(s)
- Beckett Sterner
- Center for Biology and Society, Arizona State University, PO Box 873301, Tempe, AZ, 85287-3301, USA.
| | - Scott Lidgard
- Integrative Research Center, Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
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6
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Worsaae K, Giribet G, Martínez A. The role of progenesis in the diversification of the interstitial annelid lineage Psammodrilidae. INVERTEBR SYST 2018. [DOI: 10.1071/is17063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Psammodrilidae constitutes a family of understudied, nearly completely ciliated, small-sized annelids, whose systematic position in Annelida remains unsettled and whose internal phylogeny is here investigated for the first time. Psammodrilids possess hooked chaetae typical of macroscopic tube-dwelling semi-sessile annelids, such as Arenicolidae. Yet, several minute members resemble, with their conspicuous gliding by ciliary motion and vagile lifestyle, interstitial fauna, adapted to move between sand grains. Moreover, psammodrilids exhibit a range of unique features, for example, bendable aciculae, a collar region with polygonal unciliated cells, and a muscular pumping pharynx. We here present a combined phylogeny of Psammodrilidae including molecular and morphological data of all eight described species (two described herein as Psammodrilus didomenicoi, sp. nov. and P. norenburgi, sp. nov.) as well as four undescribed species. Ancestral character state reconstruction suggests the ancestor of Psammodrilidae was a semi-sessile larger form. Miniaturisation seems to have occurred multiple times independently within Psammodrilidae, possibly through progenesis, yielding small species with resemblance to a juvenile stage of the larger species. We find several new cryptic species and generally reveal an unexpected diversity and distribution of this small family. This success may be favoured by their adaptive morphology, here indicated to be genetically susceptible to progenesis.
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7
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Gomes Rodrigues H, Cornette R, Clavel J, Cassini G, Bhullar BAS, Fernández-Monescillo M, Moreno K, Herrel A, Billet G. Differential influences of allometry, phylogeny and environment on the rostral shape diversity of extinct South American notoungulates. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171816. [PMID: 29410874 PMCID: PMC5792951 DOI: 10.1098/rsos.171816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 12/21/2017] [Indexed: 05/15/2023]
Abstract
Understanding the mechanisms responsible for phenotypic diversification, and the associated underlying constraints and ecological factors represents a central issue in evolutionary biology. Mammals present a wide variety of sizes and shapes, and are characterized by a high number of morphological convergences that are hypothesized to reflect similar environmental pressures. Extinct South American notoungulates evolved in isolation from northern mammalian faunas in highly disparate environments. They present a wide array of skeletal phenotypes and convergences, such as ever-growing dentition. Here, we focused on the origins of the rostral diversity of notoungulates by quantifying the shape of 26 genera using three-dimensional geometric morphometric analysis. We tested the influence of allometry and phylogeny on rostral shape and evaluated rates of evolutionary change in the different clades. We found strong allometric and phylogenetic signals concerning the rostral shape of notoungulates. Despite convergent forms, we observed a diffuse diversification of rostral shape, with no significant evidence of influence by large-scaled environmental variation. This contrasts with the increase in dental crown height that occurred in four late-diverging families in response to similar environmental pressures. These results illustrate the importance of considering both biological components and evolutionary rates to better understand some aspects of phenotypic diversity.
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Affiliation(s)
- Helder Gomes Rodrigues
- Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), UMR CNRS 7207, CP38, Muséum National d'Histoire Naturelle, Univ Paris 6, 8 rue Buffon, 75005 Paris, France
- Mécanismes adaptatifs et évolution (MECADEV), UMR 7179, CNRS, Funevol team, Muséum National d'Histoire Naturelle, 55 rue Buffon, Bat. Anatomie Comparée, CP 55, 75005, Paris Cedex 5, France
- Author for correspondence: Helder Gomes Rodrigues e-mail:
| | - Raphaël Cornette
- Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), MNHN, CNRS, UPMC, CP26, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
| | - Julien Clavel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, Paris Sciences et Lettres (PSL), Research University, 75005 Paris, France
| | - Guillermo Cassini
- División Mastozoología, Museo Argentino de Ciencias Naturales ‘‘Bernardino Rivadavia’’(MACN), Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Luján, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Yale University, PO Box 208109, New Haven, CT 06520, USA
| | - Bhart-Anjan S. Bhullar
- Department of Geology and Geophysics, Yale University, PO Box 208109, New Haven, CT 06520, USA
- Peabody Museum of Natural History, Yale University, 170 Whitney Avenue, New Haven, CT 06511, USA
| | - Marcos Fernández-Monescillo
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales (IANIGLA), CCT–CONICET–Mendoza, Avenida Ruiz Leal s/n, Parque Gral, San Martín 5500, Mendoza, Argentina
| | - Karen Moreno
- Instituto de Ciencias de la Tierra, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Anthony Herrel
- Mécanismes adaptatifs et évolution (MECADEV), UMR 7179, CNRS, Funevol team, Muséum National d'Histoire Naturelle, 55 rue Buffon, Bat. Anatomie Comparée, CP 55, 75005, Paris Cedex 5, France
| | - Guillaume Billet
- Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), UMR CNRS 7207, CP38, Muséum National d'Histoire Naturelle, Univ Paris 6, 8 rue Buffon, 75005 Paris, France
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8
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Roggero A, Dierkens M, Barbero E, Palestrini C. Combined phylogenetic analysis of two new Afrotropical genera of Onthophagini (Coleoptera, Scarabaeidae). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Angela Roggero
- Department of Life Sciences and Systems Biology; University of Torino; Via Accademia Albertina 13 I-10123 Torino Italy
| | | | - Enrico Barbero
- Department of Life Sciences and Systems Biology; University of Torino; Via Accademia Albertina 13 I-10123 Torino Italy
| | - Claudia Palestrini
- Department of Life Sciences and Systems Biology; University of Torino; Via Accademia Albertina 13 I-10123 Torino Italy
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9
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Giribet G, Boyer SL, Baker CM, Fernández R, Sharma PP, de Bivort BL, Daniels SR, Harvey MS, Griswold CE. A molecular phylogeny of the temperate Gondwanan family Pettalidae (Arachnida, Opiliones, Cyphophthalmi) and the limits of taxonomic sampling. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12419] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gonzalo Giribet
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Sarah L. Boyer
- Biology Department; Macalester College; 1600 Grand Avenue St. Paul MN 55105 USA
| | - Caitlin M. Baker
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Rosa Fernández
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Prashant P. Sharma
- Department of Zoology; University of Wisconsin-Madison; 352 Birge Hall, 430 Lincoln Drive Madison WI 53706 USA
| | - Benjamin L. de Bivort
- Department of Organismic and Evolutionary Biology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Savel R. Daniels
- Department of Botany and Zoology; University of Stellenbosch; Matieland Stellenbosch 7602 South Africa
| | - Mark S. Harvey
- Department of Terrestrial Zoology; Western Australian Museum; Welshpool DC WA 6986 Australia
| | - Charles E. Griswold
- Department of Entomology; California Academy of Sciences; San Francisco CA 94118 USA
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10
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Cichocka JM, Bielecki A. Phylogenetic utility of the geometric model of the body form in leeches (Clitellata: Hirudinida). Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Monjaraz-Ruedas R, Francke OF. Systematics of the genusMayazomus(Arachnida: Schizomida): the relevance of using continuous characters and pedipalp setae patterns to schizomid phylogenetics. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rodrigo Monjaraz-Ruedas
- Posgrado en Ciencias Biológicas; Universidad Nacional Autónoma de México; Avenue Universidad 3000, C.P. 04510 Coyoacán Distrito Federal México
- Colección Nacional de Arácnidos; Departamento de Zoología; Instituto de Biología; Universidad Nacional Autónoma de México; 3er. Circuito exterior s/n. Apartado Postal 70-153, C.P. 04510, Ciudad Universitaria, Coyoacán Ciudad de México Distrito Federal México
| | - Oscar F. Francke
- Colección Nacional de Arácnidos; Departamento de Zoología; Instituto de Biología; Universidad Nacional Autónoma de México; 3er. Circuito exterior s/n. Apartado Postal 70-153, C.P. 04510, Ciudad Universitaria, Coyoacán Ciudad de México Distrito Federal México
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12
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Bardin J, Rouget I, Yacobucci MM, Cecca F. Increasing the number of discrete character states for continuous characters generates well-resolved trees that do not reflect phylogeny. Integr Zool 2015; 9:531-41. [PMID: 24148350 DOI: 10.1111/1749-4877.12076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since the introduction of the cladistic method in systematics, continuous characters have been integrated into analyses but no methods for their treatment have received unanimous support. Some methods require a large number of character states to discretise continuous characters in order to keep the maximum level of information about taxa differences within the coding scheme. Our objective was to assess the impact of increasing the character state number on the outcomes of phylogenetic analyses. Analysis of a variety of simulated datasets shows that these methods for coding continuous characters can lead to the generation of well-resolved trees that do not reflect a phylogenetic signal. We call this phenomenon the flattening of the tree-length distribution; it is influenced by both the relative quantity of continuous characters in relation to discrete characters, and the number of characters in relation to the number of taxa. Bootstrap tests provide a method to avoid this potential bias.
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Affiliation(s)
- Jérémie Bardin
- Sorbonne University, Pierre-and-Marie-Curie University (UPMC-P6), Paris, France; National Museum of Natural History (MNHN), Paris, France; The National Center for Scientific Research (CNRS), Paris, France
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13
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Mongiardino Koch N, Soto IM, Ramírez MJ. Overcoming problems with the use of ratios as continuous characters for phylogenetic analyses. ZOOL SCR 2015. [DOI: 10.1111/zsc.12120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicolás Mongiardino Koch
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires
- Instituto de Ecología; Genética y Evolución de Buenos Aires (IEGEBA - CONICET/UBA); Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA); Capital Federal Buenos Aires Argentina
| | - Ignacio M. Soto
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires
- Instituto de Ecología; Genética y Evolución de Buenos Aires (IEGEBA - CONICET/UBA); Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA); Capital Federal Buenos Aires Argentina
| | - Martín J. Ramírez
- Museo Argentino de Ciencias Naturales - CONICET; Ángel Gallardo 490 (C1405 DJR) Capital Federal Buenos Aires Argentina
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14
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Lopardo L, Hormiga G. Out of the twilight zone: phylogeny and evolutionary morphology of the orb-weaving spider family Mysmenidae, with a focus on spinneret spigot morphology in symphytognathoids (Araneae, Araneoidea). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12199] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lara Lopardo
- Department of Biological Sciences; The George Washington University; 2023 G Street NW Washington DC WA 20052 USA
| | - Gustavo Hormiga
- Department of Biological Sciences; The George Washington University; 2023 G Street NW Washington DC WA 20052 USA
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Abstract
Opiliones are one of the largest arachnid orders, with more than 6,500 species in 50 families. Many of these families have been erected or reorganized in the last few years since the publication of The Biology of Opiliones. Recent years have also seen an explosion in phylogenetic work on Opiliones, as well as in studies using Opiliones as test cases to address biogeographic and evolutionary questions more broadly. Accelerated activity in the study of Opiliones evolution has been facilitated by the discovery of several key fossils, including the oldest known Opiliones fossil, which represents a new, extinct suborder. Study of the group's biology has also benefited from rapid accrual of genomic resources, particularly with respect to transcriptomes and functional genetic tools. The rapid emergence and utility of Phalangium opilio as a model for evolutionary developmental biology of arthropods serve as demonstrative evidence of a new area of study in Opiliones biology, made possible through transcriptomic data.
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Affiliation(s)
- Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138;
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16
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Boyer SL, Baker CM, Popkin-Hall ZR, Laukó DI, Wiesner HA, Quay RH. Phylogeny and biogeography of the mite harvestmen (Arachnida : Opiliones : Cyphophthalmi) of Queensland, Australia, with a description of six new species from the rainforests of the Wet Tropics. INVERTEBR SYST 2015. [DOI: 10.1071/is14025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Wet Tropics of Queensland, Australia, represent the largest remaining fragment of vast rainforests that once covered the entire continent. Over the past few decades the Wet Tropics bioregion has received much attention from biologists interested in the effect of climate change on diversity and distribution of rainforest animals. However, most such studies have focused on vertebrates, and despite considerable interest in the biota of the area, the diversity of many of Wet Tropics invertebrate taxa remains poorly known. Here we describe six new species of mite harvestman from the area, identified using a combination of morphological and molecular data. Our study represents the first detailed phylogenetic study of the genus Austropurcellia, and provides insight into the historical biogeography of these dispersal-limited arachnids.
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Koch NM, Soto IM, Ramírez MJ. First phylogenetic analysis of the family Neriidae (Diptera), with a study on the issue of scaling continuous characters. Cladistics 2014; 31:142-165. [DOI: 10.1111/cla.12084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Nicolás Mongiardino Koch
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; Ciudad Universitaria; Pabellón II (C1428 EHA) Buenos Aires Argentina
| | - Ignacio M. Soto
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; Ciudad Universitaria; Pabellón II (C1428 EHA) Buenos Aires Argentina
- Instituto de Ecología; Genética y Evolución de Buenos Aires (IEGEBA) - CONICET; Buenos Aires Argentina
| | - Martín J. Ramírez
- Museo Argentino de Ciencias Naturales - CONICET; Buenos Aires Argentina
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18
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Clouse RM, Sharma PP, Giribet G, Wheeler WC. Elongation factor-1α, a putative single-copy nuclear gene, has divergent sets of paralogs in an arachnid. Mol Phylogenet Evol 2013; 68:471-81. [PMID: 23669012 DOI: 10.1016/j.ympev.2013.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 03/21/2013] [Accepted: 04/22/2013] [Indexed: 11/17/2022]
Abstract
Identification of paralogy in candidate nuclear loci is an important prerequisite in phylogenetics and statistical phylogeography, but one that is often overlooked. One marker commonly assumed to be a single-copy gene and claimed to harbor great utility for inferring recent divergences is elongation factor-1α (EF-1α). To test this hypothesis, we systematically cloned EF-1α in three disjunct populations of the harvestman Metasiro americanus. Here we show that EF-1α has a large number of paralogs in this species. The paralogs do not evolve in a concerted manner, and the paralogs diverged prior to the population divergence. Moreover, the paralogs of M. americanus are not comparable to the highly divergent EF-1α paralogs found in bees and spiders, which are easily recognized and separated through the use of specific primers. We demonstrate statistically that our detection of paralogs cannot be attributed to amplification error. The presence of EF-1α paralogs in M. americanus prevents its use in statistical phylogeography, and the presence of out-paralogs argues against its use in phylogenetic inference among recently diverged clades. These data contradict the common assumption that EF-1α is for most or all taxa a single-copy gene, or that it has a small number of paralogs that are homogenized through gene conversion, unequal crossing over, or other processes.
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Affiliation(s)
- Ronald M Clouse
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York City, NY 10024, USA.
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19
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Smith UE, Hendricks JR. Geometric morphometric character suites as phylogenetic data: extracting phylogenetic signal from gastropod shells. Syst Biol 2013; 62:366-85. [PMID: 23325808 DOI: 10.1093/sysbio/syt002] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite being the objects of numerous macroevolutionary studies, many of the best represented constituents of the fossil record-including diverse examples such as foraminifera, brachiopods, and mollusks-have mineralized skeletons with limited discrete characteristics, making morphological phylogenies difficult to construct. In contrast to their paucity of phylogenetic characters, the mineralized structures (tests and shells) of these fossil groups frequently have distinctive shapes that have long proved useful for their classification. The recent introduction of methodologies for including continuous data directly in a phylogenetic analysis has increased the number of available characters, making it possible to produce phylogenies based, in whole or part, on continuous character data collected from such taxa. Geometric morphometric methods provide tools for accurately characterizing shape variation and can produce quantitative data that can therefore now be included in a phylogenetic matrix in a nonarbitrary manner. Here, the marine gastropod genus Conus is used to evaluate the ability of continuous characters-generated from a geometric morphometric analysis of shell shape-to contribute to a total evidence phylogenetic hypothesis constructed using molecular and morphological data. Furthermore, the ability of continuous characters derived from geometric morphometric analyses to place fossil taxa with limited discrete characters into a phylogeny with their extant relatives was tested by simulating the inclusion of fossil taxa. This was done by removing the molecular partition of individual extant species to produce a "cladistic pseudofossil" with only the geometric morphometric derived characters coded. The phylogenetic position of each cladistic pseudofossil taxon was then compared with its placement in the total evidence tree and a symmetric resampling tree to evaluate the degree to which morphometric characters alone can correctly place simulated fossil species. In 33-45% of the test cases (depending upon the approach used for measuring success), it was possible to place the pseudofossil taxon into the correct regions of the phylogeny using only the morphometric characters. This suggests that the incorporation of extinct Conus taxa into phylogenetic hypotheses will be possible, permitting a wide range of macroevolutionary questions to be addressed within this genus. This methodology also has potential to contribute to phylogenetic reconstructions for other major components of the fossil record that lack numerous discrete characters.
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Affiliation(s)
- Ursula E Smith
- Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA.
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MAGALHÃES IVANLF, SANTOS ADALBERTOJ. Phylogenetic analysis of Micrathena and Chaetacis spiders (Araneae: Araneidae) reveals multiple origins of extreme sexual size dimorphism and long abdominal spines. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00831.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
21
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de Bivort BL, Clouse RM, Giribet G. A cladistic reconstruction of the ancestral mite harvestman (Arachnida, Opiliones, Cyphophthalmi): portrait of a Paleozoic detritivore. Cladistics 2012; 28:582-597. [DOI: 10.1111/j.1096-0031.2012.00407.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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22
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GIRIBET GONZALO, SHARMA PRASHANTP, BENAVIDES LIGIAR, BOYER SARAHL, CLOUSE RONALDM, DE BIVORT BENJAMINL, DIMITROV DIMITAR, KAWAUCHI GISELEY, MURIENNE JEROME, SCHWENDINGER PETERJ. Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01774.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
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