scholarly journals Dissecting host-associated communities with DNA barcodes

2016 ◽  
Vol 371 (1702) ◽  
pp. 20150328 ◽  
Author(s):  
Christopher C. M. Baker ◽  
Leonora S. Bittleston ◽  
Jon G. Sanders ◽  
Naomi E. Pierce
Keyword(s):  
Species Interactions ◽  
Morphological Characters ◽  
South American ◽  
Dna Barcodes ◽  
Substantial Variation ◽  
East African ◽  
Pitcher Plant ◽  
Genome Data ◽  
Symbiotic Interactions ◽  
Database Connectivity

DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia ( Acacia ) drepanolobium ; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes . Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data. This article is part of the themed issue ‘From DNA barcodes to biomes’.

scholarly journals Revision of the poorly known Neotropical butterfly genus Zischkaia Forster, 1964 (Lepidoptera, Nymphalidae, Satyrinae), with descriptions of nine new species

2019 ◽  
Author(s):  
Shinichi Nakahara ◽  
Thamara Zacca ◽  
Fernando M.S. Dias ◽  
Diego R. Dolibaina ◽  
Lei Xiao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Dna Sequence ◽  
Sequence Data ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
South American ◽  
Dna Barcodes ◽  
Dna Sequence Data

We provide the first comprehensive taxonomic revision of the poorly known South American butterfly genus Zischkaia Forster, 1964, hitherto regarded as including three described species. A phylogenetic analysis based on DNA sequence data shows that Zischkaia is monophyletic and consists of two morphologically diagnosable clades. Morphological characters and DNA ‘barcodes’ support the recognition of twelve species in the genus, a significant increase even for the relatively poorly studied subtribe Euptychiina. Consequently, nine new species are described and named herein, including Z. arctoa Nakahara, sp. nov., Z. chullachaki Nakahara & Zacca, sp. nov., Z. baku Zacca, Dolibaina & Dias, sp. nov., Z. arenisca Nakahara, Willmott & Hall, sp. nov., Z. argyrosflecha Nakahara, L. Miller & Huertas, sp. nov., Z. abanico Nakahara & Petit, sp. nov., Z. josti Nakahara & Kleckner, sp. nov., Z. mielkeorum Dolibaina, Dias & Zacca, sp. nov. and Z. warreni Dias, Zacca & Dolibaina, sp. nov. In addition, a neotype is designated for Satyrus pacarus Godart, [1824], and lectotypes are designated for Euptychia amalda Weymer, 1911, Euptychia fumata Butler, 1867 and Euptychia saundersii Butler, 1867.

Beyond Wallace: a new lineage of Chrysorthenches (Lepidoptera: Yponomeutoidea: Glyphipterigidae) reveals a journey tracking its host-plants, Podocarpus (Pinopsida: Podocarpaceae)

2020 ◽  
Vol 190 (2) ◽  
pp. 709-736
Author(s):  
Jae-Cheon Sohn ◽  
Shigeki Kobayashi ◽  
Yutaka Yoshiyasu
Keyword(s):  
Maximum Likelihood ◽  
East Asia ◽  
Host Plants ◽  
Morphological Characters ◽  
Species Group ◽  
Geological History ◽  
Dna Barcodes ◽  
History Of ◽  
Species Groups ◽  
Maximum Likelihood Phylogeny

Abstract A northward trans-Wallacean radiation is demonstrated for Chrysorthenches, a member of the Orthenches group. Here we review Chrysorthenches and allied genera resulting in a generic transfer of Diathryptica callibrya to Chrysorthenches and two new congeners: C. muraseaeSohn & Kobayashisp. nov. from Japan and C. smaragdinaSohnsp. nov. from Thailand. We review morphological characters of Chrysorthenches and allied genera, and find polyphyly of Diathryptica and the association of the Orthenches-group with Glyphipterigidae. These findings were supported in a maximum likelihood phylogeny of DNA barcodes from ten yponomeutoids. We analysed 30 morphological characters for 12 species of Chrysorthenches, plus one outgroup, via a cladistic approach. The resulting cladogram redefined two pre-existing Chrysorthenches species-groups and identified one novel lineage: the C. callibrya species-group. We review the host associations between Chrysorthenches and Podocarpaceae, based on mapping the working phylogenies. Our review suggests that ancestral Chrysorthenches colonized Podocarpus and later shifted to other podocarp genera. Biogeographical patterns of Chrysorthenches show that they evolved long after the Podocarpaceae radiation. Disjunctive trans-Wallacean distribution of the C. callibrya species-group is possibly related to the tracking of their host-plants and the complicated geological history of the island-arc system connecting Australia and East Asia.

Salicornia cuscoensis (Amaranthaceae/Chenopodiaceae), a new species from Peru (South America)

Phytotaxa ◽  
2017 ◽  
Vol 319 (3) ◽  
pp. 254 ◽  
Author(s):  
M. ÁNGELES ALONSO ◽  
MANUEL B. CRESPO ◽  
HELMUT FREITAG
Keyword(s):  
New Species ◽  
South America ◽  
Morphological Characters ◽  
Tierra Del Fuego ◽  
South American ◽  
Habitat Distribution ◽  
Closely Related Species ◽  
Molecular Analyses ◽  
Southern Patagonia ◽  
A New Species

The name Salicornia cuscoensis given to a plant from high Andean saltmarshes near Cusco [Cuzco] and Ayacucho, Peru (South America) is validated by a diagnosis and description. The main morphological characters that separate S. cuscoensis from other closely related species are creeping habit, delicate branches, inflorescence of short and thin spikes, and seed indumentum. The new species clearly differs from other perennial Salicornia taxa growing in high Andean saltmarshes such as S. pulvinata and S. andina. The former forms small compact cushions producing very short, few-flowered inflorescences. The latter shows woody stems and forms larger rounded carpets. Morphologically, S. cuscoensis is also similar to S. magellanica, a species growing along the seashore in southern Patagonia and Tierra del Fuego, but the latter has shorter and wider inflorescences and larger seeds with a different type and arrangement of indumentum. Molecular analyses also supported the separation of S. cuscoensis. Data on habitat, distribution and phylogenetic relationships are presented for the new species and its relatives, and an identification key is given for the South American taxa of the genus Salicornia.

Taxonomic status of Andersen’s fruit-eating bat (Artibeus jamaicensis aequatorialis) and revised classification of Artibeus (Chiroptera: Phyllostomidae)

Zootaxa ◽  
2010 ◽  
Vol 2648 (1) ◽  
pp. 45 ◽  
Author(s):  
PETER A. LARSEN ◽  
MARÍA R. MARCHÁN-RIVADENEIRA ◽  
ROBERT J. BAKER
Keyword(s):  
Taxonomic Status ◽  
Morphological Characters ◽  
Species Level ◽  
South American ◽  
Reciprocal Monophyly ◽  
Dna Variation ◽  
The Andes ◽  
Artibeus Jamaicensis ◽  
Phylogenetic Studies

Fruit-eating bats of the genus Artibeus are widely distributed across the Neotropics and are one of the most recently evolved assemblages of the family Phyllostomidae. Although the taxonomy and systematics of species of Artibeus has been the subject of an intense historical debate, the most current taxonomic arrangements recognize approximately eleven species within the genus. However, recent phylogenetic studies indicate that species diversity within South and Middle American populations of Artibeus is underestimated. South American populations referable to A. jamaicensis aequatorialis are of considerable interest because previous studies of mitochondrial DNA variation identified potential species level variation west of the Andes Mountains. In this study we use morphometric and genetic data (nuclear AFLPs) to investigate the taxonomic status of A. j. aequatorialis. Our results indicate that elevating aequatorialis to species level is appropriate based on statistically supported reciprocal monophyly in mitochondrial and nuclear datasets and diagnostic morphological characters. In light of our results, and of those presented elsewhere, we provide a revised classification of the genus.

Taxonomy of the Sylvilagus brasiliensis complex in Central and South America (Lagomorpha: Leporidae)

2019 ◽  
Vol 100 (5) ◽  
pp. 1599-1630 ◽  
Author(s):  
Luis A Ruedas ◽  
Sofia Marques Silva ◽  
Johnnie H French ◽  
Roy Nelson Platt ◽  
Jorge Salazar-Bravo ◽  
...  
Keyword(s):  
South America ◽  
Morphological Characters ◽  
Molecular Data ◽  
Type Material ◽  
Valid Species ◽  
South American ◽  
Species Status ◽  
Neotropical Species ◽  
Nomen Dubium ◽  
Taxonomic Framework

Abstract A taxonomic framework for South American cottontail rabbits (Lagomorpha: Leporidae: Sylvilagus) was recently published by Diersing and Wilson (2017). Although we agree with some of its taxonomic conclusions (e.g., species status for S. apollinaris and S. fulvescens), we disagree with others. We provide herein evidence supporting S. andinus as a valid species based on morphological characters and novel molecular data. We also provide details of the morphological characters of S. apollinaris and S. fulvescens that support separating these from S. brasiliensis. We adduce data suggestive to the effect that—absent any type material—S. defilippi is at best a nomen dubium. Finally, we provide evidence in support of recognizing additional Neotropical species of Sylvilagus. Un esquema taxonómico para los conejos sudamericanos (Lagomorpha: Leporidae: Sylvilagus) fue recientemente publicado por Diersing y Wilson (2017). Aunque estamos de acuerdo con algunas de sus conclusiones (por ejemplo: estatus de especie válida para S. apollinaris y S. fulvescens), no estamos de acuerdo con las restantes conclusiones taxonómicas. Aportamos aquí pruebas convincentes sobre la característica naturaleza de los caracteres morfológicos y moleculares de S. andinus, pruebas que esgrimimos en apoyo de la hipótesis que esta última es una especie válida, así confirmando su escisión de S. brasiliensis. Proporcionamos detalles de los caracteres morfológicos de S. apollinaris y S. fulvescens que confirman la decisión taxonómica de asimismo separarlos de S. brasiliensis. Proporcionamos datos en aditamento que indican que a falta de cualquier material tipo para S. defilippi, este nombre es en el mejor de los casos un nomen dubium. Finalmente, ofrecemos datos y evidencia apoyando nuestras decisiones de reconocer un mayor número de especies Neotropicales de Sylvilagus que previamente se conocían.

scholarly journals Identification key to the Anopheles mosquitoes of South America (Diptera: Culicidae). III. Male genitalia

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Maria Anice Mureb Sallum ◽  
Ranulfo González Obando ◽  
Nancy Carrejo ◽  
Richard C. Wilkerson
Keyword(s):  
South America ◽  
Species Identification ◽  
Male Genitalia ◽  
Morphological Characters ◽  
Identification Key ◽  
Careful Examination ◽  
South American ◽  
Type Specimens ◽  
South American Species ◽  
Accurate Identification

Abstract Background Accurate identification of the species of Anopheles Meigen, 1818 requires careful examination of all life stages. However, morphological characters, especially those of the females and fourth-instar larvae, show some degree of polymorphism and overlap among members of species complexes, and sometimes even within progenies. Characters of the male genitalia are structural and allow accurate identification of the majority of species, excluding only those in the Albitarsis Complex. In this key, based on the morphology of the male genitalia, traditionally used important characters are exploited together with additional characters that allow robust identification of male Anopheles mosquitoes in South America. Methods Morphological characters of the male genitalia of South American species of the genus Anopheles were examined and employed to construct a comprehensive, illustrated identification key. For those species for which specimens were not available, illustrations were based on published illustrations. Photographs of key characters of the genitalia were obtained using a digital Canon Eos T3i attached to a light Diaplan Leitz microscope. The program Helicon Focus was used to build single in-focus images by stacking multiple images of the same structure. Results An illustrated key to South American species of Anopheles based on the morphology of the male genitalia is presented, together with a glossary of morphological terms. The male genitalia of type-specimens of previously poorly documented species were also examined and included in the key, e.g. Anopheles (Anopheles) tibiamaculatus (Neiva, 1906) which has a unique quadrangular-shaped aedeagus with an apical opening. Conclusions Male genitalia of South American species of Anopheles possess robust characters that can be exploited for accurate species identification. Distortion that can occur during the dissection and mounting process can obstruct accurate identification; this is most evident with inadvertent damage or destruction of unique features and interferes with correctly assigning shapes of the features of the ventral claspette. In some species, the shape, and anatomical details of the aedeagus also need to be examined for species identification. For members of the Myzorhynchella Series, both ventral and dorsal claspettes possess multiple characteristics that are herein used as reliable characters for species identification.

Systematics of reptile-associated scale mites of the genus Pterygosoma (Acariformes: Pterygosomatidae) derived from external morphology

Zootaxa ◽  
2019 ◽  
Vol 4603 (3) ◽  
pp. 401
Author(s):  
MONIKA FAJFER
Keyword(s):  
North Africa ◽  
New Genus ◽  
Arabian Peninsula ◽  
Morphological Characters ◽  
Mite Species ◽  
South American ◽  
The Family ◽  
Outgroup Species ◽  
Tree Lizards ◽  
Species Groups

The phylogeny of the mite genus Pterygosoma Peters, 1849 (Acariformes: Pterygosomatidae), permanent parasites of lizards of the families Agamidae, Gerrhosauridae and Liolaemidae (Reptilia: Squamata), was inferred with maximum parsimony, successive weighting and implied weighting approaches based on 182 characters of 48 ingroup and 12 outgroup species. All undertaken analyses questioned the monophyly of the genus. Based on this research, Pterygosoma includes 56 mite species associated with agamas from Africa and Asia (Sauria: Agamidae). Within the genus seven natural species groups were found: mutabilis, inermis, melanum, caucasica, fimbriata, singularis and foliosetis; 13 species of the genus were not assigned to any of the groups due to their unique morphological characters. For the ligare group of the subgenus Pterygosoma s. str. (7 species) associated with the South American tree lizards from the family Liolaemidae, a new genus, Neopterygosoma gen. nov., is established. The subgenus Gerrhosaurobia Lawrence, 1959 (3 species) associated with the African plated lizards of the family Gerrhosauridae is elevated to the genus rank. Diagnoses for the three genera are presented. Historical associations are reconstructed by fitting the obtained mite tree into the host topology on the family level. Results of coevolutionary analysis highlight the coincidence of both trees. The studies suggest that the ancestor of the genus Pterygosoma switched from the hosts of Gerrhosaurobia i.e. from the plated lizards (Gerrhosauridae) to the agamas (Agamidae), and the genus Pterygosoma has its biogeographic origin in North Africa, and colonized Asia via the Arabian Peninsula, which is congruent with the historical biogeography of its hosts.

scholarly journals A fully web-illustrated morphological phylogenetic study of relationships among oak gall wasps and their closest relatives (Hymenoptera: Cynipidae)

Zootaxa ◽  
2008 ◽  
Vol 1796 (1) ◽  
pp. 1 ◽  
Author(s):  
JOHAN LILJEBLAD ◽  
FREDRIK RONQUIST ◽  
JOSE-LUIS NIEVES-ALDREY ◽  
FELIX FONTAL-CAZALLA ◽  
PALMIRA ROS-FARRE ◽  
...  
Keyword(s):  
Morphological Characters ◽  
Phylogenetic Study ◽  
Character State ◽  
South American ◽  
Japanese Species ◽  
Modern Information Technology ◽  
Morphological Studies ◽  
Gall Wasps ◽  
Two Generations ◽  
Galling Insects

Large morphological phylogenetics analyses are often poorly documented because of the constraints of traditional print journals, making it difficult to critically evaluate the data and build on it in future studies. We use modern information technology to overcome this problem in a comprehensive analysis of higher relationships among oak gall wasps and their closest relatives. Our morphological characters are documented by more than 2,000 images deposited in the open web image database Morphbank (http://www.morphbank.net), allowing one-click access from character and character state descriptions to the raw data. The oak gall wasps (Cynipidae: Cynipini) form one of the largest specialized radiations of galling insects with almost 1,000 described species attacking oaks or oak relatives. According to previous morphological studies, the Cynipini form a monophyletic clade, the Woody Rosid Gallers (WRG), together with three small cynipid tribes (Diplolepidini, Eschatocerini, and Pediaspidini). The WRG all attack woody representatives of the rosid clade of eudicots. Little was previously known about higher WRG relationships. We studied 54 exemplar taxa of WRG, including representatives from 34 of the 41 valid genera of oak gall wasps, and two outgroups. The study resulted in 308 characters, 283 from morphology and 25 from biology and distribution; most of these are original to the present paper. Parsimony analyses supported the monophyly of three major WRG lineages: Diplolepidini + Eschatocerini, Pediaspidini + Paraulax, and Cynipini. The poorly known South American genus Paraulax, developing in galls on Nothofagus, is moved from Cynipini to Pediaspidini to reflect these results. The single Japanese species described in Paraulax by Shinji (types lost) is transferred to Ceroptres as C. quereicola (Shinji 1938) comb. nov. Two major lineages of oak gallers were recognized in most analyses: (1) the Neuroterus-group (Neuroterus, Pseudoneuroterus, the previously recognized genus Trichagalma, Plagiotrochus, possibly also Palearctic Dryocosmus and Aphelonyx+Disholcaspis); and (2)the Cynips-group (Cynips, Belonocnema, Atrusca, Acraspis, Philonix, Biorhiza and Trigonaspis). The large and problematic genus Andricus was paraphyletic in some analyses and monophyletic in others, with Disholcaspis spectabilis being the sister to other Cynipini in the former case and European Callirhytis in the latter. Our results suggest that WRG are conservative in their host plant preferences but there is no evidence for parallel insect-plant cladogenesis. Distributional patterns suggest a possible origin for the oak gall wasps in the Nearctic but the picture is otherwise complicated. Both heterogeny, the cyclical alternation of sexual and parthenogenetic generations, and heteroecy, the use of different sections of Quercus as host for the two generations, appear to have evolved twice within the WRG.

scholarly journals Morphometric and phylogenetic analyses of Serpentirhabdias viperidicus n. sp. (Nematoda: Rhabdiasidae) from the lancehead snake Bothrops moojeni Hoge, 1966 (Reptilia: Serpentes: Viperidae) in Brazil

2016 ◽  
Vol 91 (3) ◽  
pp. 360-370 ◽  
Author(s):  
D.H. Morais ◽  
A. Aguiar ◽  
M.I. Müller ◽  
R.B. Narciso ◽  
L.A.F. da Silva ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Neotropical Region ◽  
South American ◽  
Paulo State ◽  
Molecular Approaches ◽  
Molecular Phylogenetic ◽  
Bothrops Moojeni ◽  
A New Species

AbstractSerpentirhabdias viperidicus n. sp. (Nematoda: Rhabdiasidae) is described from the lungs of the ‘Brazilian lancehead’ Bothrops moojeni (Hoge, 1966) from the savannah in São Paulo State, Brazil. The new species is the eighth species of Serpentirhabdias described in the Neotropical region, and differs from other species mainly by a combination of characters: lips slightly notable, presence of fine striations at posterior ends, presence of two parallel lines with intercalated pores, a pore-shaped phasmid situated at the level of the anal aperture and another two in the posterior half of the tail. It is the first species of Serpentirhabdias reported in this snake host and the second species of this genus found parasitizing South American viperidian snakes. Molecular phylogenetic analysis using ribosomal (ITS and 28S partial) genes confirms Serpentirhabdias viperidicus n. sp. as a new species that clustered in the Serpentirhabdias clade, sister taxon to Serpentirhabdias fuscovenosa and Serpentirhabdias elaphe. This is the first description of Serpentirhabdias species from Brazil using molecular approaches and morphological characters to confirm the monophyly of this recent genus.

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