A redescription and phylogenetic analysis based on new material of the fossil newtsTaricha oligocenicaVan Frank, 1955 andTaricha lindoeiNaylor, 1979 (Amphibia, Salamandridae) from the Oligocene of Oregon

2018 ◽  
Vol 92 (4) ◽  
pp. 713-733
Author(s):  
John J. Jacisin ◽  
Samantha S.B. Hopkins
Keyword(s):  
Phylogenetic Analysis ◽  
Population Level ◽  
Morphological Characters ◽  
Morphological Data ◽  
Neural Spine ◽  
Separate Species ◽  
Skeletal Morphology ◽  
New Material ◽  
John Day

AbstractComplete body fossils of salamanders are relatively rare, but provide critical information on the evolutionary roots of extant urodele clades. We describe new specimens of the fossil salamandridsTaricha oligocenicaVan Frank, 1955, andTaricha lindoeiNaylor, 1979, from the Oligocene Mehama and John Day formations of Oregon that illustrate aspects of skeletal morphology previously unseen in these taxa, and contribute to our understanding of population-level variation. Morphological analysis of these specimens supports the classification ofT.oligocenicaandT.lindoeias two different species, distinct from extantTaricha. Parsimony-based, heuristic analysis of phylogeny using 108 morphological characters for 40 taxa yields different results from a phylogenetic analysis that excludes four taxa known only via vertebrae. Our smaller analysis generally agrees with molecular phylogenies of the family Salamandridae, but with poorer resolution for molgin newts, especially betweenTarichaandNotophthalmus. The analysis including all taxa produced polytomies mostly related to complications from several fossil taxa. The presence or absence of dorsally expanded, sculptured neural spine tables on trunk vertebrae, an important character in past descriptions of fossil salamandrids, appears to be either homoplastic within the Salamandridae, or requires an expansion of characters or character states.Taricha oligocenicaandT. lindoeiare separate species of an at least 33 million-year-old clade, but their relationships with each other and extant North American salamandrids remain unclear with current levels of morphological data. Salamandrid research requires additional morphological data, particularly for the vertebrae and ribs, to better resolve salamandrid evolutionary history through morphological characters.

The first record of the trematode Urogonimus certhiae (Trematoda: Leucochloridiidae) in the Eurasian nuthatch Sitta europaea

2020 ◽  
Vol 29 (2) ◽  
pp. 238-246
Author(s):  
E.E. Prokhorova ◽  
A.A. Vinogradova ◽  
A.S. Tokmakova ◽  
G.L. Ataev
Keyword(s):  
Phylogenetic Analysis ◽  
First Record ◽  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Morphological Data ◽  
Its2 Rdna ◽  
Separate Species ◽  
Sitta Europaea

Adult trematodes of the genus Urogonimus Monticelli, 1888 were found in the cloaca of a male Eurasian nuthatch Sitta europaea Linnaeus, 1758, the carcass of which was found in the Vyritsa Settlm. (Leningrad Prov., Northwest Russia). Based on morphological characters, the worms were identified as U. certhiae McIntosh, 1927. This is the first record of this parasite from the nuthatch and from Northwest Russia. We analysed nucleotide sequences of ITS1-5.8S-ITS2 rDNA of this species and found important differences with U. macrostomus (Rudolphi, 1803). Genetic and morphological data indicated that U. certhiae and U. macrostomus were two separate species. Phylogenetic analysis confirmed that Urogonimus and Leucochloridium Carus, 1835 were two distinct genera.

scholarly journals Salticidae (Arachnida, Araneae) of Thailand: new species and records of Epeus Peckham & Peckham, 1886 and Ptocasius Simon, 1885

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9352
Author(s):  
Barbara Maria Patoleta ◽  
Joanna Gardzińska ◽  
Marek Żabka
Keyword(s):  
New Species ◽  
Natural History ◽  
Morphological Characters ◽  
Natural History Museum ◽  
Morphological Data ◽  
History Museum ◽  
Two New Species ◽  
New Material ◽  
Hungarian Natural History Museum ◽  
Three New Species

The study is based on new material from the collections of the Naturalis Biodiversity Centre in Leiden (RNHM) and the Hungarian Natural History Museum (HNHM) and addresses issues in two genera: Epeus Peckham & Peckham, 1886 and Ptocasius Simon, 1885 from Thailand. Both genera are of Asian/Indomalayan origin, the latter with a diversity hotspot in the subtropical valleys of the Himalayas. Based on morphological data, we propose three new species of Epeus (Epeus daiqini sp. nov. (♂♀), Epeus pallidus sp. nov. (♀), Epeus szirakii sp. nov. (♀)) and two new species of Ptacasius (Ptocasius metzneri sp. nov. (♂♀) and Ptocasius sakaerat sp. nov. (♀)). Additionally, we redescribed E. tener (Simon, 1877) and added photographs of morphological characters. The genus Ptocasius is redefined due to the inclusion of 37 species, previously included in Yaginumaella Prószyński, 1979. Relationships and distribution of both genera are discussed in reference to molecular, morphological and distributional data, published by other authors in recent years.

A redefinition of the genus Troglocharinus Reitter, 1908, with description of new species (Coleoptera, Leiodidae, Cholevinae, Leptodirini)

Zootaxa ◽  
2021 ◽  
Vol 4926 (2) ◽  
pp. 151-188
Author(s):  
JAVIER FRESNEDA ◽  
VALERIA RIZZO ◽  
JORDI COMAS ◽  
IGNACIO RIBERA
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Valid Species ◽  
Distribution Area ◽  
Undescribed Species ◽  
Separate Species ◽  
Male And Female ◽  
New Material

We redefine the genus Troglocharinus Reitter, 1908 based on a phylogenetic analysis with a combination of mitochondrial and molecular data. We recovered the current Speonomites mengeli (Jeannel, 1910) and S. mercedesi (Zariquiey, 1922) as valid, separate species within the Troglocharinus clade, not directly related to Speonomites Jeannel, 1910, a finding corroborated by a detailed study of the male and female genitalia. In consequence, we reinstate Speonomus mercedesi Zariquiey, 1922 stat. nov. as a valid species, transfer both of them to the genus Troglocharinus, T. mengeli (Jeannel, 1910) comb. nov. and T. mercedesi (Zariquiey, 1922) comb. nov., and redescribe the genus. The study of new material from the distribution area of the former S. mengeli revealed the presence of two undescribed species, T. sendrai sp. nov. and T. fadriquei sp. nov., which we describe herein. We designate the lectotype of Speonomus vinyasi Escolà, 1971 to fix its identity, as among its syntypes there are two different species. In agreement with the results of the phylogenetic analyses we establish the synonymy between the genus Speonomites and Pallaresiella Fresneda, 1998 syn. nv. 

New insights on the taxonomy and phylogenetic relationships of the Neotropical genus Phoebis (Pieridae: Coliadinae) revealed by molecular and morphological data

Zootaxa ◽  
2018 ◽  
Vol 4457 (1) ◽  
pp. 179 ◽  
Author(s):  
LEIDYS MURILLO-RAMOS ◽  
RENZO HERNÁNDEZ TORRES ◽  
RAYNER NÚÑEZ ÁGUILA ◽  
ROGER AYAZO
Keyword(s):  
Morphological Characters ◽  
Point Of View ◽  
Morphological Data ◽  
Caribbean Region ◽  
Greater Antilles ◽  
Data Set ◽  
Mitochondrial Coi ◽  
The Matrix ◽  
Taxonomic Point

Phoebis Hübner (1819) is a genus of the Neotropical subfamily Coliadinae (Lepidoptera: Pieridae). The highest diversity is found in the Greater Antilles islands in the Caribbean region. Although from the taxonomic point of view, Phoebis seems to be a stable genus, there is no phylogenetic hypothesis corroborating the monophyly of the genus. In this study, we used both morphological characters and a genetic dataset consisting of one mitochondrial (COI) and three nuclear markers (RpS5, MDH, Wingless). The matrix was concatenated and analysed with parsimony under implied weights (IW). Also, the concatenated data set was analysed using maximum likelihood and Bayesian inference evolutionary methods, and ancestral states reconstruction with characters traditionally used for classification of Phoebis was carried out. The same topology was recovered by Parsimony, ML and BI analysis, and suggest that Phoebis is not a monophyletic genus, with Aphrissa and Rhabdodryas nested within it. Our findings allow us to consider the genera Rhabdodryas syn.rev. and Aphrissa syn.rev. to be synonyms of Phoebis. These results have implications for the systematics of Phoebis and the genera that should be accepted in Coliadinae.

Characterisation of the Australian Nacophorini using adult morphology, and phylogeny of the Geometridae based on morphological characters

Zootaxa ◽  
2008 ◽  
Vol 1736 (1) ◽  
pp. 1 ◽  
Author(s):  
CATHERINE J. YOUNG
Keyword(s):  
Phylogenetic Analysis ◽  
Majority Rule ◽  
Morphological Character ◽  
Morphological Characters ◽  
Data Sources ◽  
Morphological Data ◽  
Bootstrap Support ◽  
Consensus Tree ◽  
Molecular Analyses ◽  
Character Set

The Australian Nacophorini and related taxa are described using a matrix of 116 adult morphological characters. Adults of 72 species are illustrated using photographs and electron micrographs. Subsets of the characters are used to conduct a phylogenetic analysis based on cladistic principles. The adult morphological character set was augmented with 17 characters from eggs and 27 from larvae. The resulting phylogeny is poorly resolved but provides support for many of the relationships recovered by previous molecular analyses of the group, including basal derivations for characters of Larentiinae and Sterrhinae relative to those of the rest of Geometridae, and the monophyly of the Geometrinae + Oenochrominae s. str. Combining 28S D2 datawith morphological data produced a matrix of 60 taxa and 590 characters. The majority rule consensus tree produced by the combined morphological and 28S D2 data is almost identical to the majority rule consensus tree produced by the 28S D2 data alone, except that bootstrap support is lower for most nodes. Common clades obtained from the molecular and morphological trees are described in terms of morphological data. On this basis a concept of the Australian Nacophorini includes Lithinini and Australian Archiearinae. Two robust groups within the tribe also are delimited using characters from all data sources. Comparsions are made between the Nearctic and Neotropical Nacophorini on the basis of shared morphological characters. Australian Boarmiini are defined by synapomorphies.

scholarly journals Phylogenetic Signal and Bias in Paleontology

2021 ◽  
Author(s):  
Robert J Asher ◽  
Martin R Smith
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Tree Of Life ◽  
Morphological Data ◽  
Phylogenetic Resolution ◽  
Phylogeny Estimation ◽  
Better Than

Abstract An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.

scholarly journals First Report of Podosphaera aphanis Causing Powdery Mildew on Wild Blackberry Species (Rubus spp.) in Mexico

Plant Disease ◽  
2021 ◽  
Author(s):  
Alma Rosa Solano-Báez ◽  
Santos Gerardo Leyva-Mir ◽  
Moises Camacho-Tapia ◽  
Alfonso Arellano Victoria ◽  
Geremias Rodríguez-Bautista ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Powdery Mildew ◽  
Primary Source ◽  
Morphological Characters ◽  
Morphological Data ◽  
Wild Populations ◽  
First Report ◽  
Voucher Specimens ◽  
New Varieties ◽  
Germ Tubes

Wild blackberry species (Rubus spp. L.; Rosaceae) represents an invaluable source of genes for the generation of new varieties, but also serve as a primary source of disease inoculum. During April of 2020, symptoms of powdery mildew were observed on four populations of wild blackberry species located in the states of Chiapas (16°59'11"N, 92°59'07"W; 16°47'08"N, 92°31'05"W) and Michoacán (19°37'17"N, 100°08'59"W; 19°29'25"N, 101°32'54"W), Mexico. Signs of the pathogen were white powdery masses mainly on the top of new shoots. Symptoms included yellowing, necrosis, and early defoliation of the plants. Hyphae were tin-walled, hyaline, smooth, and 4.0–9.0 mm wide. Appressoria were indistinct -to- nipple-shaped. Conidiophores (n=30, 75–225 × 10.5–13.5 μm) were straight, and unbranched with cylindrical foot cells (n=30, 31.5–158 × 8–13.5 μm), straight, somewhat widening upwards, followed by 1–3 shorter cells. Conidia (n=100; 25.5–38.5 × 9.5–22.5 μm) were catenulate, ellipsoid-ovoid -to- doliiform, containing fibrosin bodies (in 3% KOH). Germ tubes (n=30, 13.5–40.5 × 4.5 μm) emerged laterally, and were unbranched with slightly swollen tips. Chasmothecia were not found. Morphological characters of the fungus in all samples corresponded to the previous descriptions of Podosphaera aphanis by Braun and Cook (2012) and Stevanovi´c et al. (2020). Voucher specimens were deposited in the Department of Agricultural Parasitology Herbarium at the Chapingo Autonomous University under accessions UACH421, UACH423, UACH425, UACH426. To confirm the species identification, the internal transcribed spacer (ITS) of one sample was amplified using the primers ITS5 (White et al. 1990) and P3 (Kusaba and Tsuge, 1995) and sequenced. The sequence was deposited in GenBank (accession number MW988591). A phylogenetic analysis using Bayesian inference and maximum likelihood was performed (Hernández-Restrepo et al. 2018) and included other Podosphaera species (Takamatsu et al. 2010). The sequence from the isolate UACH426 clustered with the strain MUMH1871 of P. aphanis forming a definite clade and remained as a sister taxon of P. pannosa. Pathogenicity was verified through inoculation by gently dusting conidia from one powdery mildew patch onto leaves of five healthy blackberry plants of each specie. The same number of noninoculated plants served as controls. All plants were maintained in a greenhouse at 25–30°C with 75% relative humidity. All inoculated plants developed powdery mildew symptoms after 12 days, whereas no symptoms were observed on noninoculated plants. The fungus recovered from the inoculated plants was morphologically identical to that originally observed on diseased blackberry plants, demonstrating the pathogenicity of the fungus. Based on morphological data and phylogenetic analysis, the fungus was identified as P. aphanis. This fungus has been reported to cause powdery mildew on blackberry plants in Serbia (Stevanovi´c et al. 2020). This is the first report of P. aphanis causing powdery mildew on wild backberry species in Mexico according to Farr and Rossman (2021). The primary source of inoculum of powdery mildew for commercial plantings is wild blackberry plants from noncultivated areas and may warrant control of wild populations.

scholarly journals Markov models provide many solutions for appropriate modeling of inapplicable morphological characters in phylogenetics

2021 ◽  
Author(s):  
Sergei Tarasov
Keyword(s):  
Phylogenetic Analysis ◽  
Markov Models ◽  
Main Type ◽  
Morphological Characters ◽  
Bayesian Framework ◽  
Morphological Data ◽  
New Models

AbstractThis paper describes new models for coding inapplicable characters for phylogenetic analysis with morphological data. I show that these new solutions fall into two categories that require use of different Markov models. Their implementation in the Bayesian framework using popular software RevBayes (Höhna et al., 2016) is provided. A combination of the new models and previous solutions (Tarasov, 2019) is capable to model all main type of dependencies between morphological characters.

scholarly journals Craniodental morphology and phylogeny of marsupials

2021 ◽  
Author(s):  
Robin M. D. Beck ◽  
Robert Voss ◽  
Sharon Jansa
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Future Research ◽  
Data Types ◽  
Wide Range ◽  
Morphological And Molecular Data ◽  
Dense Sampling

The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with relatively limited sampling of Recent and fossil taxa, and many studies based on analyses of molecular data that include a dense sampling of Recent taxa, but relatively few that combine both data types. Another dichotomy in the marsupial phylogenetic literature is between studies that focus on New World taxa, others that focus on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna, based on combined analyses of morphology and molecular sequences, for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 species representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) taxa represented by well-preserved fossils, and 5 outgroups (non-marsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3 and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., †Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., †Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology, including descriptions and illustrations of some features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters, and improved methods of phylogenetic analysis.

The phylogeny and classification of the tribe Halictini, with special reference to the Halictus genus-group (Hymenoptera: Halictidae)

2004 ◽  
Vol 13 (1) ◽  
pp. 83-113
Author(s):  
Yu.A. Pesenko
Keyword(s):  
Phylogenetic Analysis ◽  
Male Genitalia ◽  
Posterior Margin ◽  
Sister Group ◽  
Morphological Characters ◽  
Species Group ◽  
Transverse Ridge ◽  
Inner Surface ◽  
Paraphyletic Group

The monophyly of the cosmopolitan tribe Halictini, including over 2300 currently recognized species, is supported by at least a single manifested synapomorphy shared by all members of the tribe: metasomal tergum VII of the male is modified; this forms a transverse ridge giving a false apex beneath which the tergum is strongly reflexed to the morphological posterior margin. On the basis of the present phylogenetic analysis, the tribe Halictini is subdivided into five subtribes: Halictina (comprised of 7 genera: Echthralictus, Glossodialictus, Halictus, Homalictus, Patellapis, Seladonia, and Thrincohalictus), Sphecodina (4 genera: Eupetersia, Microsphecodes, Ptilocleptis, and Sphecodes), Thrinchostomina (2 genera: Thrinchostoma and Parathrincostoma), Caenohalictina (9 genera: Agapostemon, Caenohalictus, Dinagapostemon, Habralictus, Mexalictus, Paragapostemon, Pseudagapostemon, Rhinetula, and Ruizantheda), and Gastrohalictina (one large and diverse genus: Lasioglossum s. l.). The subtribe Halictina is a paraphyletic group; the remaining four tribes are strictly monophyletic (holophyletic). The monophyly of the Halictus genus-group, comprising the genera Halictus and Seladonia, is supported by two distinct synapomorphies of the male genitalia: (1) dorsal gonostylus simple (not double), flattened, broad, narrowed proximally, and provided with a clump of very coarse bristles on the inner surface; (2) ventral gonostylus sclerotized, relatively thin and long, directed backward. Only generalized members of the group possess both the character states above. In derived members, the clump of bristles and the ventral gonostylus are often lost independently. The sister group of the Halictus genus-group is the genus Thrincohalictus. This is supported by the following synapomorphy found among the tribe Halictini only in Halictus, Seladonia, and Thrincohalictus: the ventral gonobasal rim in the male genitalia is forming a right posterolateral angle with a short projection directed laterally. Another feature characterizing these three genera is the presence (except in the parasitic subgenus Paraseladonia) of posterior bands of tomentum or dense and much plumose appressed hairs on the metasomal terga. However, this character is shared also with Patellapis subgenera Patellapis and Lomatalictus. The following subgeneric classification of the genera Halictus and Seladonia is suggested. The genus Halictus includes 12 subgenera: Acalcaripes (2 species), Argalictus (8), Halictus s. str. (4), Hexataenites (11), Lampralictus (1), Monilapis (29), Nealictus (2), Odontalictus (2), Platyhalictus (14), Protohalictus (13), Ramalictus (2), and Tytthalictus (4). The genus Seladonia comprises 6 subgenera, including 2 new ones: Mucoreohalictus subg. n. (15), Pachyceble (22), Paraseladonia (1), Placidohalictus subg. n. (5), Seladonia s. str. (36), and Vestitohalictus (16). The subgenera of Halictus and Seladonia are keyed. The phylogenetic tree of the subgenera of Halictus and Seladonia is reconstructed with use of 46 morphological characters of adults. All other genera of the tribe Halictini were taken as outgroup. The genus Halictus is ascertained as a strictly monophyletic group based upon a single postulated synapomorphy: dorsal gonostylus with a triangular hair patch as a distal appendage on inner side. All the subgenera of this genus appear as strictly monophyletic groups, with the exception of Monilapis, which is a paraphyletic one in relation to Acalcaripes. The monophyly of the genus Seladonia is supported by three synapomorphies, including a novelty (unique synapomorphy): male dorsal gonostylus with a deep cleft. All the subgenera of this genus are strictly monophyletic with the exception of Placidohalictus, which is a paraphyletic one in relation to Vestitohalictus and Mucoreohalictus. A synonymical catalogue of species and species-group names in the genera Halictus and Seladonia, including 442 names, is provided as an appendix.

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