DrosoPhyla: resources for Drosophilid Phylogeny and Systematics.
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ABSTRACT:
SUBMITTER: Finet C
PROVIDER: S-EPMC8382681 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The genus Phytopythium (Peronosporales) has been described, but a complete circumscription has not yet been presented. In the present paper we provide molecular-based evidence that members of Pythium clade K as described by Lévesque & de Cock (2004) belong to Phytopythium. Maximum likelihood and Bayesian phylogenetic analysis of the nuclear ribosomal DNA (LSU and SSU) and mitochondrial DNA cytochrome oxidase subunit 1 (COI) as well as statistical analyses of pairwise distances strongly support the status of Phytopythium as a separate phylogenetic entity. Phytopythium is morphologically intermediate between the genera Phytophthora and Pythium. It is unique in having papillate, internally proliferating sporangia and cylindrical or lobate antheridia. The formal transfer of clade K species to Phytopythium and a comparison with morphologically similar species of the genera Pythium and Phytophthora is presented. A new species is described, Phytopythium mirpurense.
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Project description:Xiphosurans are aquatic chelicerates with a fossil record extending into the Early Ordovician and known from a total of 88 described species, four of which are extant. Known for their apparent morphological conservatism, for which they have gained notoriety as supposed 'living fossils', recent analyses have demonstrated xiphosurans to have an ecologically diverse evolutionary history, with several groups moving into non-marine environments and developing morphologies markedly different from those of the modern species. The combination of their long evolutionary and complex ecological history along with their paradoxical patterns of morphological stasis in some clades and experimentation among others has resulted in Xiphosura being of particular interest for macroevolutionary study. Phylogenetic analyses have shown the current taxonomic framework for Xiphosura-set out in the Treatise of Invertebrate Paleontology in 1955-to be outdated and in need of revision, with several common genera such as Paleolimulus Dunbar, 1923 and Limulitella Størmer, 1952 acting as wastebasket taxa. Here, an expanded xiphosuran phylogeny is presented, comprising 58 xiphosuran species as part of a 158 taxon chelicerate matrix coded for 259 characters. Analysing the matrix under both Bayesian inference and parsimony optimisation criteria retrieves a concordant tree topology that forms the basis of a genus-level systematic revision of xiphosuran taxonomy. The genera Euproops Meek, 1867, Belinurus König, 1820, Paleolimulus, Limulitella, and Limulus are demonstrated to be non-monophyletic and the previously synonymized genera Koenigiella Raymond, 1944 and Prestwichianella Cockerell, 1905 are shown to be valid. In addition, nine new genera (Andersoniella gen. nov., Macrobelinurus gen. nov., and Parabelinurus gen. nov. in Belinurina; Norilimulus gen. nov. in Paleolimulidae; Batracholimulus gen. nov. and Boeotiaspis gen. nov. in Austrolimulidae; and Allolimulus gen. nov., Keuperlimulus gen. nov., and Volanalimulus gen. nov. in Limulidae) are erected to accommodate xiphosuran species not encompassed by existing genera. One new species, Volanalimulus madagascarensis gen. et sp. nov., is also described. Three putative xiphosuran genera-Elleria Raymond, 1944, Archeolimulus Chlupáč, 1963, and Drabovaspis Chlupáč, 1963-are determined to be non-xiphosuran arthropods and as such are removed from Xiphosura. The priority of Belinurus König, 1820 over Bellinurus Pictet, 1846 is also confirmed. This work is critical for facilitating the study of the xiphosuran fossil record and is the first step in resolving longstanding questions regarding the geographic distribution of the modern horseshoe crab species and whether they truly represent 'living fossils'. Understanding the long evolutionary history of Xiphosura is vital for interpreting how the modern species may respond to environmental change and in guiding conservation efforts.
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Project description:Species of Calonectria are important plant pathogens, several of which have a worldwide distribution. Contemporary taxonomic studies on these fungi have chiefly relied on DNA sequence comparisons of the beta-tubulin gene region. Despite many new species being described, there has been no phylogenetic synthesis for the group since the last monographic study almost a decade ago. In the present study, the identity of a large collection of Calonectria isolates from various geographic regions was determined using morphological and DNA sequence comparisons. This resulted in the discovery of seven new species; Ca. densa, Ca. eucalypti, Ca. humicola, Ca. orientalis, Ca. pini, Ca. pseudoscoparia and Ca. sulawesiensis, bringing the total number of currently accepted Calonectria species to 68. A multigene phylogeny was subsequently constructed for all available Calonectria spp., employing seven gene regions, namely actin, beta-tubulin, calmodulin, histone H3, the internal transcribed spacer regions 1 and 2 and the 5.8S gene of the ribosomal RNA, 28S large subunit RNA gene and translation elongation 1-alpha. Based on these data 13 phylogenetic groups could be distinguished within the genus Calonectria that correlated with morphological features. Dichotomous and synoptic keys to all Calonectria spp. currently recognised are also provided.
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Project description:IntroductionClonostachys, a genus with rich morphological and ecological diversity in Bionectriaceae, has a wide distribution among diverse habitats.Methods and resultsIn the present study, a phylogenetic framework is reconstructed for the family Bionectriaceae focusing on Clonostachys through increased taxon-sampling using the nrLSU sequence. Through surveying Clonostachys in China, Vietnam, and Thailand over the past 3 years, seven Clonostachys spp. were found and identified. Two new species, C. chuyangsinensis and C. kunmingensis, are described and illustrated based on morphological characteristics and molecular data. The phylogenetic positions of the seven species were evaluated based on four genomic loci (ITS, nrLSU, TUB2, and TEF1).DiscussionMoreover, the genetic divergence comparisons of Clonostachys species for three markers (ITS, TUB2, and TEF1) are also provided. The results indicated that the TEF1 sequence data provided the best resolution for distinguishing species of Clonostachys, followed by sequence data for the TUB2 and ITS regions.
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Project description:Thirteen morphologically similar strains of barbatosphaeria- and tectonidula-like fungi were studied based on the comparison of cultural and morphological features of sexual and asexual morphs and phylogenetic analyses of five nuclear loci, i.e. internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA, β-tubulin, and second largest subunit of RNA polymerase II. Phylogenetic results were supported by in-depth comparative analyses of common core secondary structure of ITS1 and ITS2 in all strains and the identification of non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript. Barbatosphaeria is defined as a well-supported monophyletic clade comprising several lineages and is placed in the Sordariomycetes incertae sedis. The genus is expanded to encompass nine species with both septate and non-septate ascospores in clavate, stipitate asci with a non-amyloid apical annulus and non-stromatic ascomata with a long decumbent neck and carbonised wall often covered by pubescence. The asexual morphs are dematiaceous hyphomycetes with holoblastic conidiogenesis belonging to Ramichloridium and Sporothrix types. The morphologically similar Tectonidula, represented by the type species T. hippocrepida, grouped with members of Barbatosphaeria and is transferred to that genus. Four new species are introduced and three new combinations in Barbatosphaeria are proposed. A dichotomous key to species accepted in the genus is provided.
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Project description:The taxonomy and phylogeny of the genus Tolypocladium are herein revised based on the most comprehensive dataset to date. Two species-level phylogenies of Tolypocladium were constructed: a single-gene phylogeny (ITS) of 35 accepted species and a multigene phylogeny (nrSSU, nrLSU, tef-1α, rpb1, and rpb2) of 27 accepted species. Three new species, Tolypocladium pseudoalbum sp. nov., Tolypocladium subparadoxum sp. nov., and Tolypocladium yunnanense sp. nov., are described in the present study. The genetic divergences of four markers (ITS, tef-1α, rpb1 and rpb2) among Tolypocladium species are also reported. The results indicated that species of Tolypocladium were best delimited by rpb1 sequence data, followed by the sequence data for the rpb2, tef-1α, and ITS provided regions. Finally, a key to the 48 accepted species of Tolypocladium worldwide is provided.
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Project description:The family Lumbricidae is arguably the most well-known and well-studied earthworm group due to its dominance in the European earthworm fauna and its invasion in temperate regions worldwide. However, its North American members, especially the genus Bimastos Moore, 1893, are poorly understood. We revised the systematics of the genus Bimastos and tested the hypothesis of the monophyly of North American lumbricids using morphological characters and eight molecular markers. Phylogenetic analyses based on our extensive sampling of Bimastos and inclusion of Dendrodrilus and Allolobophoridella indicated a well-supported clade containing Bimastos and Eisenoides Gates, 1969, and provided the first evidence supporting that North American lumbricids are monophyletic. Assuming the available divergence time estimations and dating of land bridges are correct, it would suggest that the ancestor of this clade arrived North America through Beringia or the De Geer route during Late Cretaceous, and since then the clade has diverged from its Eurasian sister group, Eisenia. The peregrine genera Dendrodrilus and Allolobophoridella are nested within the Bimastos clade; we propose to treat them as junior synonyms of the genus Bimastos, and, contradictory to the commonly held belief of being European, they are indeed part of the indigenous North American earthworm fauna. Morphological characters, such as red-violet pigmentation, proclinate U-shaped nephridial bladders and calciferous diverticula in segment 10 further support this placement. The East Mediterranean-Levantine Spermophorodrilus Bouché, 1975 and Healyella Omodeo & Rota, 1989 are nested within the Dendrobaena sensu lato clade; therefore their close relationship with the North American Bimastos is refuted. Species fit the revised diagnosis of Bimastos are reviewed and keyed, and a new species, Bimastos schwerti sp. nov., is described.
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Project description:Three approaches to molecular phylogenetics are demonstrated to biology students as they explore molecular data from Homo sapiens and four related primates. By analyzing DNA sequences, protein sequences, and chromosomal maps, students are repeatedly challenged to develop hypotheses regarding the ancestry of the five species. Although these exercises were designed to supplement and enhance classroom instruction on phylogeny, cladistics, and systematics in the context of a postsecondary majors-level introductory biology course, the activities themselves require very little prior student exposure to these topics. Thus, they are well suited for students in a wide range of educational levels, including a biology class at the secondary level. In implementing this exercise, we have observed measurable gains, both in student comprehension of molecular phylogeny and in their acceptance of modern evolutionary theory. By engaging students in modern phylogenetic activities, these students better understood how biologists are currently using molecular data to develop a more complete picture of the shared ancestry of all living things.
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Project description:Our current knowledge on the crocodyliform evolution is strongly biased towards the skull morphology, and the postcranial skeleton is usually neglected in many taxonomic descriptions. However, it is logical to expect that it can contribute with its own phylogenetic signal. In this paper, the changes in the tree topology caused by the addition of the postcranial information are analysed for the family Allodaposuchidae, the most representative eusuchians in the latest Cretaceous of Europe. At present, different phylogenetic hypotheses have been proposed for this group without reaching a consensus. The results of this paper evidence a shift in the phylogenetic position when the postcranium is included in the dataset, pointing to a relevant phylogenetic signal in the postcranial elements. Finally, the phylogenetic relationships of allodaposuchids within Eusuchia are reassessed; and the internal relationships within Allodaposuchidae are also reconsidered after an exhaustive revision of the morphological data. New and improved diagnoses for each species are here provided.
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