scholarly journals The phylogenetics of Teleosauroidea (Crocodylomorpha, Thalattosuchia) and implications for their ecology and evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9808 ◽  
Author(s):  
Michela M. Johnson ◽  
Mark T. Young ◽  
Stephen L. Brusatte
Keyword(s):  
Phylogenetic Analyses ◽  
Species Level ◽  
Data Matrix ◽  
Bayesian Analyses ◽  
New Family ◽  
Coastal Marine ◽  
Poor Understanding ◽  
Phylogenetic Hypotheses ◽  
One New Species ◽  
Shed Light

Teleosauroidea was a clade of ancient crocodylomorphs that were a key element of coastal marine environments during the Jurassic. Despite a 300-year research history and a recent renaissance in the study of their morphology and taxonomy, macroevolutionary studies of teleosauroids are currently limited by our poor understanding of their phylogenetic interrelationships. One major problem is the genus Steneosaurus, a wastebasket taxon recovered as paraphyletic or polyphyletic in phylogenetic analyses. We constructed a newly updated phylogenetic data matrix containing 153 taxa (27 teleosauroids, eight of which were newly added) and 502 characters, which we analysed under maximum parsimony using TNT 1.5 (weighted and unweighted analyses) and Bayesian inference using MrBayes v3.2.6 (standard, gamma and variation). The resulting topologies were then analysed to generate comprehensive higher-level phylogenetic hypotheses of teleosauroids and shed light on species-level interrelationships within the clade. The results from our parsimony and Bayesian analyses are largely consistent. Two large subclades within Teleosauroidea are recovered, and they are morphologically, ecologically and biogeographically distinct from one another. Based on comparative anatomical and phylogenetic results, we propose the following major taxonomic revisions to Teleosauroidea: (1) redefining Teleosauridae; (2) introducing one new family and three new subfamilies; (3) the resurrection of three historical genera; and (4) erecting seven new generic names and one new species name. The phylogeny infers that the Laurasian subclade was more phenotypically plastic overall than the Sub-Boreal-Gondwanan subclade. The proposed phylogeny shows that teleosauroids were more diverse than previously thought, in terms of morphology, ecology, dispersal and abundance, and that they represented some of the most successful crocodylomorphs during the Jurassic.

scholarly journals The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7430
Author(s):  
Kumiko Matsui ◽  
Takanobu Tsuihiji
Keyword(s):  
Phylogenetic Analyses ◽  
Data Matrix ◽  
Common Ancestry ◽  
Consensus Trees ◽  
Phylogenetic Hypotheses ◽  
Aquatic Mammals ◽  
Data Matrices

Background Desmostylia is a clade of extinct aquatic mammals with no living members. Today, this clade is considered belonging to either Afrotheria or Perissodactyla. In the currently-accepted taxonomic scheme, Desmostylia includes two families, 10 to 12 genera, and 13–14 species. There have been relatively few phylogenetic analyses published on desmostylian interrelationship compared to other vertebrate taxa, and two main, alternative phylogenetic hypotheses have been proposed in previous studies. One major problem with those previous studies is that the numbers of characters and OTUs were small. Methods In this study, we analyzed the phylogenetic interrelationship of Desmostylia based on a new data matrix that includes larger numbers of characters and taxa than in any previous studies. The new data matrix was compiled mainly based on data matrices of previous studies and included three outgroups and 13 desmostylian ingroup taxa. Analyses were carried out using five kinds of parsimonious methods. Results Strict consensus trees of the most parsimonious topologies obtained in all analyses supported the monophyly of Desmostylidae and paraphyly of traditional Paleoparadoxiidae. Based on these results, we propose phylogenetic definitions of the clades Desmostylidae and Paleoparadoxiidae based on common ancestry.

Larval chaetotaxy and morphology are highly homoplastic yet phylogenetically informative in Hydrobiusini water scavenger beetles (Coleoptera: Hydrophilidae)

2020 ◽  
Author(s):  
Miguel Archangelsky ◽  
Nicolás Rafael Martínez Román ◽  
Martin Fikáček
Keyword(s):  
Phylogenetic Analyses ◽  
Head Capsule ◽  
Data Matrix ◽  
Larval Morphology ◽  
Morphometric Characters ◽  
Molecular Analyses ◽  
Adult Morphology ◽  
Phylogenetic Hypotheses

Abstract Phylogenetic analyses testing the monophyly of the tribe Hydrobiusini and the relationships among its genera are performed based on a data matrix including characters of larval morphology and morphometrics, larval chaetotaxy and adult morphology, including eight of the nine hydrobiusine genera plus 15 outgroup taxa. The head chaetotaxy of six genera of the tribe Hydrobiusini is described (Ametor, Hybogralius, Hydramara, Limnohydrobius, Limnoxenus and Sperchopsis). Morphometric characters derived from the head capsule and mouthparts are included. All characters are illustrated in detail. The analyses performed on the above datasets and their combinations reveal the monophyly of the Hydrobiusini except for Hybogralius, and reconstruct the internal topology of the tribe, largely corresponding to results of previous molecular analyses. Hybogralius groups with genera having larvae adapted to underwater feeding in all analyses. The position of the genus Tritonus within the Laccobiini is questioned by our analyses, which suggest a closer relationship with the tribes Hydrophilini or Hydrobiusini. Larval characters are revealed as highly homoplastic, with chaetotaxic characters performing slightly worse than usual larval morphology. Nonetheless, they are phylogenetically informative and useful for testing phylogenetic hypotheses resulting from analyses of molecules or adult morphology. A key to larvae of the genera of the Hydrobiusini is presented.

Iodosphaeria honghense sp. nov. (Iodosphaeriaceae, Xylariales) from Yunnan Province, China

Phytotaxa ◽  
2019 ◽  
Vol 420 (4) ◽  
pp. 273-282
Author(s):  
DIANA S. MARASINGHE ◽  
MILAN C. SAMARAKOON ◽  
SINANG HONGSANAN ◽  
SARANYAPHAT BOONMEE ◽  
ERIC H. C. MCKENZIE
Keyword(s):  
Maximum Likelihood ◽  
Yunnan Province ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Data Matrix ◽  
Bayesian Analyses ◽  
Mucilaginous Sheath ◽  
Distinct Lineage

Iodosphaeria honghense sp. nov., collected from dead twigs of an unknown host in Honghe, Yunnan Province, China, is introduced based on morphological characteristics and phylogenetic analyses. Iodosphaeria honghense is distinct from other similar taxa in having cylindrical to allantoid, guttulate ascospores without a mucilaginous sheath. Maximum likelihood and Bayesian analyses based on combined LSU, ITS and RPB2 data matrix indicate that I. honghense forms a distinct lineage within the Iodosphaeriaceae. This study provides a detailed description and illustrations with morphological comparisons, and includes a key to accepted Iodosphaeria species.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

New olenelline trilobites from the Northwest Territories, Canada, and the phylogenetic placement of Judomia absita Fritz, 1973

Zootaxa ◽  
2011 ◽  
Vol 2918 (1) ◽  
pp. 15 ◽  
Author(s):  
I. WESLEY GAPP ◽  
BRUCE S. LIEBERMAN ◽  
MICHAEL C. POPE ◽  
KELLY A. DILLIARD
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Northwest Territories ◽  
Phylogenetic Analyses ◽  
Geographic Range ◽  
Early Cambrian ◽  
Phylogenetic Placement ◽  
The Subject ◽  
Three New Species ◽  
One New Species

The Early Cambrian olenelline trilobites are a diverse clade and have been the subject of several phylogenetic analyses. Here, three new species of Bradyfallotaspis Fritz, 1972 (B. coriae, B. nicolascagei, and B. sekwiensis) and one new species of Nevadia Walcott, 1910 (N. saupeae) are described from the Sekwi Formation of the Mackenzie Mountains, Northwest Territories, Canada. In addition, new specimens potentially referable to Nevadia ovalis McMenamin, 1987 were recovered that may expand that species’ geographic range, which was thought to be restricted to Sonora, Mexico. The results of a phylogenetic analysis incorporating several olenelline taxa, including Judomia absita Fritz, 1973 from the Sekwi Formation, are also presented herein. This species has been assigned to various olenelline genera, including Judomia Lermontova, 1951 and Paranevadella Palmer & Repina, 1993. Phylogenetic analysis suggests this species is closely related to Judomia tera Lazarenko, 1960 from Siberia. This phylogenetic relationship provides further support for the hypothesis that a close biogeographic relationship existed between Laurentia and Siberia during the Cambrian.

Asian Betylobraconinae (Hymenoptera, Braconidae), with description of a new genus and phylogenetic affinities of the tribe Facitorini

2008 ◽  
Vol 39 (2) ◽  
pp. 133-154 ◽  
Author(s):  
Alberto Sáez ◽  
Kaoru Maeto ◽  
Alejandro Zaldivar-Riverón ◽  
Sergey Belokobylskij
Keyword(s):  
New Species ◽  
Type Species ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
28S Rrna ◽  
Asian Region ◽  
Molecular Phylogenetic ◽  
Phylogenetic Affinities ◽  
One New Species ◽  
Rrna Sequences

AbstractThe taxonomy of the Asian genera of the subfamily Betylobraconinae, a small and understudied group within the hymenopteran family Braconidae, is revised. A new genus exclusively from the Asian region, Asiabregma gen. nov., containing three species (A. ryukyuensis sp. nov. (type species, Japan and Malaya), A. makiharai sp. nov. (Japan) and A. sulaensis (van Achterberg), comb. nov. (Indonesia)) is described. One new species of Aulosaphobracon, A. striatus sp. nov. from Vietnam, and one of Facitorus, F. amamioshimus sp. nov. from Japan, are also described. Based on molecular phylogenetic analyses using COI mtDNA and 28S rRNA sequences, the three genera previously placed in the tribe Facitorini, Facitorus, Conobregma and Jannya, together with Asiabregma gen. nov., are transferred to the rogadine tribe Yeliconini.

A new species of genus Hexacentrus Serville, 1831 from Taiwan (Orthoptera: Tettigoniidae: Hexacentrinae)

Zootaxa ◽  
2021 ◽  
Vol 4933 (4) ◽  
pp. 543-556
Author(s):  
PO-WEI CHEN ◽  
HUI-CONG XIE ◽  
XUE WU ◽  
CHU-ZE SHEN ◽  
ZHU-QING HE
Keyword(s):  
New Species ◽  
Gene Tree ◽  
Species Level ◽  
National Museum ◽  
Type Specimens ◽  
As Species ◽  
Wide Range ◽  
Similar Appearance ◽  
One New Species ◽  
A New Species

There are 29 species or subspecies in genus Hexacentrus occurring in Asia, Africa and Australia. Because of its similar appearance, it is not easy to distinguish them by traditional methods. In this study, we collected samples and sequenced COI genes from wide range. By reconstructing the gene tree, we found one new species, H. formosanus Chen et He sp. nov., from Taiwan. The new species is similar to H. expansus or H. inflatissimus, but differs from the former in male Cu2 vein of left tegmina curved and slender, and spectrum of male left tegmina slender and subsquare; differs from the later by body size smaller and female tegmina narrow and short. The type specimens are deposited in National Museum of Natural Science, Taichung, Taiwan (NMNS). H. japonicus hareyamai is treated as species level, H. hareyamai stat. nov. 

scholarly journals Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov.

2020 ◽  
Vol 44 (1) ◽  
pp. 161-205
Author(s):  
J.C. Zamora ◽  
S. Ekman
Keyword(s):  
Species Level ◽  
Single Locus ◽  
Phenotypic Characters ◽  
New Family ◽  
Multispecies Coalescent ◽  
Morphometric Analyses ◽  
Methodological Approaches ◽  
First Time ◽  
A New Species ◽  
Multilocus Phylogeny

We present a multilocus phylogeny of the class Dacrymycetes, based on data from the 18S, ITS, 28S, RPB1, RPB2, TEF-1α, 12S, and ATP6 DNA regions, with c. 90 species including the types of most currently accepted genera. A variety of methodological approaches was used to infer phylogenetic relationships among the Dacrymycetes, from a supermatrix strategy using maximum likelihood and Bayesian inference on a concatenated dataset, to coalescence-based calculations, such as quartet-based summary methods of independent single-locus trees, and Bayesian integration of single-locus trees into a species tree under the multispecies coalescent. We evaluate for the first time the taxonomic usefulness of some cytological phenotypic characters, i.e., vacuolar contents (vacuolar bodies and lipid bodies), number of nuclei of recently discharged basidiospores, and pigments, with especial emphasis on carotenoids. These characters, along with several others traditionally used for the taxonomy of this group (basidium shape, presence and morphology of clamp connections, morphology of the terminal cells of cortical/marginal hyphae, presence and degree of ramification of the hyphidia), are mapped on the resulting phylogenies and their evolution through the class Dacrymycetes discussed. Our analyses reveal five lineages that putatively represent five different families, four of which are accepted and named. Three out of these four lineages correspond to previously circumscribed and published families (Cerinomycetaceae, Dacrymycetaceae, and Unilacrymaceae), and one is proposed as the new family Dacryonaemataceae. Provisionally, only a single order, Dacrymycetales, is accepted with in the class. Furthermore, the systematics of the two smallest families, Dacryonaemataceae and Unilacrymaceae, are investigated to the species level, using coalescence-based species delimitation on multilocus DNA data, and a detailed morphological study including morphometric analyses of the basidiospores. Three species are accepted in Dacryonaema, the type, Da. rufum, the newly combined Da. macnabbii (basionym Dacrymyces macnabbii), and a new species named Da. macrosporum. Two species are accepted in Unilacryma, the new U. bispora, and the type, U. unispora, the latter treated in a broad sense pending improved sampling across the Holarctic.

scholarly journals Fenestelloid clades of the Cucurbitariaceae

2020 ◽  
Vol 44 (1) ◽  
pp. 1-40
Author(s):  
W.M. Jaklitsch ◽  
H. Voglmayr
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Fungal Species ◽  
Lsu Rdna ◽  
Phylogenetic Structure ◽  
Protein Coding ◽  
Molecular Phylogenetic ◽  
Type Studies ◽  
Asexual Morphs ◽  
One New Species

Fresh collections and their ascospore and conidial isolates backed up by type studies and molecular phylogenetic analyses of a multigene matrix of partial nuSSU-, complete ITS, partial LSU rDNA, rpb2, tef1 and tub2 sequences were used to evaluate the boundaries and species composition of Fenestella and related genera of the Cucurbitariaceae. Eight species, of which five are new, are recognised in Fenestella s.str., 13 in Parafenestella with eight new species and two in the new genus Synfenestella with one new species. Cucurbitaria crataegi is combined in Fenestella, C. sorbi in Synfenestella, Fenestella faberi and Thyridium salicis in Parafenestella. Cucurbitaria subcaespitosa is distinct from C. sorbi and combined in Neocucurbitaria. Fenestella minor is a synonym of Valsa tetratrupha, which is combined in Parafenestella. Cucurbitaria marchica is synonymous with Parafenestella salicis, Fenestella bavarica with S. sorbi, F. macrospora with F. media, and P. mackenziei is synonymous with P. faberi, and the latter is lectotypified. Cucurbitaria sorbi, C. subcaespitosa and Fenestella macrospora are lecto- and epitypified, Cucurbitaria crataegi, Fenestella media, F. minor and Valsa tetratrupha are epitypified in order to stabilise the names in their phylogenetic positions. A neotype is proposed for Thyridium salicis. A determinative key to species is given. Asexual morphs of fenestelloid fungi are phoma-like and do not differ from those of other representatives of the Cucurbitariaceae. The phylogenetic structure of the fenestelloid clades is complex and can only be resolved at the species level by protein-coding genes, such as rpb2, tef1 and tub2. All fungal species studied here occur, as far as has been possible to determine, on members of Diaporthales, most frequently on asexual and sexual morphs of Cytospora.

scholarly journals Discovery of a new family of amphibians from northeast India with ancient links to Africa

2012 ◽  
Vol 279 (1737) ◽  
pp. 2396-2401 ◽  
Author(s):  
Rachunliu G. Kamei ◽  
Diego San Mauro ◽  
David J. Gower ◽  
Ines Van Bocxlaer ◽  
Emma Sherratt ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Northeast India ◽  
Sister Group Relationship ◽  
New Family ◽  
Ancient Lineage ◽  
Molecular Phylogenetic ◽  
Threatened Habitats

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

Sign in / Sign up

Export Citation Format

Share Document