The monophyly of Susisuchidae (Crocodyliformes) and its phylogenetic placement in Neosuchia.
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ABSTRACT:
SUBMITTER: Turner AH
PROVIDER: S-EPMC4330912 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Crocodyliformes is a group with a broad fossil record, in which several morphological changes have been documented. Among known transformations the most iconic is perhaps the series of changes seen in the structural evolution of the choanae. The change in the position of the choanae was important during the evolutionary history of the Crocodyliformes. This structure is relevant in the phylogenetic position of many crocodyliforms. The new skull of Susisuchus anatoceps from the Crato Formation of the Santana Group (Lower Cretaceous) is described and the preservation in the ventral view allows character encoding not yet observed for the species. The new specimen shows a typical eusuchian palate for Susisuchus anatoceps, in which the choana is fully enclosed by the pterygoid. The Susisuchidae clade has been placed in different phylogenetic positions: as a sister group of Eusuchia, advanced Neosuchia and in Eusuchia. In Isisfordia there are reports that the choana of this taxon is or is not fully enclosed by the pterygoid. The encoding of the ventral characters of S. anatoceps places Susisuchidae in Eusuchia. However, this position must be further studied, since the matrices showed fragility in the reconstitution of the Neosuchia-Eusuchia transition.
| S-EPMC6089207 | biostudies-literature
Project description:MotivationConsider a simple computational problem. The inputs are (i) the set of mixed reads generated from a sample that combines two organisms and (ii) separate sets of reads for several reference genomes of known origins. The goal is to find the two organisms that constitute the mixed sample. When constituents are absent from the reference set, we seek to phylogenetically position them with respect to the underlying tree of the reference species. This simple yet fundamental problem (which we call phylogenetic double-placement) has enjoyed surprisingly little attention in the literature. As genome skimming (low-pass sequencing of genomes at low coverage, precluding assembly) becomes more prevalent, this problem finds wide-ranging applications in areas as varied as biodiversity research, food production and provenance, and evolutionary reconstruction.ResultsWe introduce a model that relates distances between a mixed sample and reference species to the distances between constituents and reference species. Our model is based on Jaccard indices computed between each sample represented as k-mer sets. The model, built on several assumptions and approximations, allows us to formalize the phylogenetic double-placement problem as a non-convex optimization problem that decomposes mixture distances and performs phylogenetic placement simultaneously. Using a variety of techniques, we are able to solve this optimization problem numerically. We test the resulting method, called MIxed Sample Analysis tool (MISA), on a varied set of simulated and biological datasets. Despite all the assumptions used, the method performs remarkably well in practice.Availability and implementationThe software and data are available at https://github.com/balabanmetin/misa and https://github.com/balabanmetin/misa-data.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC7355250 | biostudies-literature
Project description:BACKGROUND:Molecular phylogenetic analyses have revealed that Hexapoda and Crustacea form a common clade (the Pancrustacea), which is now widely accepted among zoologists; however, the origin of Hexapoda remains unresolved. The main problems are the unclear relationships among the basal hexapod lineages, Protura (proturans), Collembola (springtails), Diplura (diplurans), and Ectognatha (bristletails, silverfishes, and all winged insects). Mitogenomic analyses have challenged hexapod monophyly and suggested the reciprocal paraphyly of Hexapoda and Crustacea, whereas studies based on nuclear molecular data support the monophyletic origin of hexapods. Additionally, there are significant discrepancies with respect to these issues between the results of morphological and molecular studies. To investigate these problems, we performed phylogenetic analyses of Pancrustacea based on the protein sequences of three orthologous nuclear genes encoding the catalytic subunit of DNA polymerase delta and the largest and second largest subunits of RNA polymerase II from 64 species of arthropods, including representatives of all hexapod orders. RESULTS:Phylogenetic analyses were conducted based on the inferred amino acid (aa) sequences (~3400 aa in total) of the three genes using the maximum likelihood (ML) method and Bayesian inference. Analyses were also performed with additional datasets generated by excluding long-branch taxa or by using different outgroups. These analyses all yielded essentially the same results. All hexapods were clustered into a common clade, with Branchiopoda as its sister lineage, whereas Crustacea was paraphyletic. Within Hexapoda, the lineages Ectognatha, Palaeoptera, Neoptera, Polyneoptera, and Holometabola were each confirmed to be monophyletic with robust support, but monophyly was not supported for Entognatha (Protura?+?Collembola?+?Diplura), Ellipura (Protura?+?Collembola), or Nonoculata (Protura?+?Diplura). Instead, our results showed that Protura is the sister lineage to all other hexapods and that Diplura or Diplura?+?Collembola is closely related to Ectognatha. CONCLUSION:This is the first study to include all hexapod orders in a phylogenetic analysis using multiple nuclear protein-coding genes to investigate the phylogeny of Hexapoda, with an emphasis on Entognatha. The results strongly support the monophyletic origin of hexapods but reject the monophyly of Entognatha, Ellipura, and Nonoculata. Our results provided the first molecular evidence in support of Protura as the sister group to other hexapods. These findings are expected to provide additional insights into the origin of hexapods and the processes involved in the adaptation of insects to life on land.
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Project description:Paratrichaptum accuratum is a large conspicuous polypore fungus growing on dead or living angiosperm trees in subtropical-boreal areas of China, Indonesia, Japan, and Taiwan. The present study places P. accuratum in the family Gloeophyllaceae that belongs to the order Gloeophyllales within Agaricomycetes (Basidiomycota), based on evidence derived from morphological and ecological characteristics, and phylogenetic analyses of sequences of nuclear rDNA regions (5.8S, nuc 18S, nuc 28S) and protein-coding genes (rpb1, rpb2, and tef1). The analyses presented in this study also give strong support for including Jaapia in Gloeophyllaceae and Gloeophyllales. Thus, the names Jaapiaceae and Jaapiales are considered here as synonyms of Gloeophyllaceae and Gloeophyllales. Since Paratrichaptum represents the earliest diverging lineage in Gloeophyllales, pileate basidiocarps and brown rot appear to be ancestral states of Gloeophyllales. Paratrichaptum accuratum may represent a relic species, according to its phylogenetic position, peculiar distribution pattern and rare occurrence.
| S-EPMC7250016 | biostudies-literature
Project description:The species-rich family Mycosphaerellaceae contains considerable morphological diversity and includes numerous anamorphic genera, many of which are economically important plant pathogens. Recent revisions and phylogenetic research have resulted in taxonomic instability. Ameliorating this problem requires phylogenetic placement of type species of key genera. We present an examination of the type species of the anamorphic Asperisporium and Pantospora. Cultures isolated from recent port interceptions were studied and described, and morphological studies were made of historical and new herbarium specimens. DNA sequence data from the ITS region and nLSU were generated from these type species, analysed phylogenetically, placed into an evolutionary context within Mycosphaerellaceae, and compared to existing phylogenies. Epitype specimens associated with living cultures and DNA sequence data are designated herein. Asperisporium caricae, the type of Asperisporium and cause of a leaf and fruit spot disease of papaya, is closely related to several species of Passalora including P. brachycarpa. The status of Asperisporium as a potential generic synonym of Passalora remains unclear. The monotypic genus Pantospora, typified by the synnematous Pantospora guazumae, is not included in Pseudocercospora sensu stricto or sensu lato. Rather, it represents a distinct lineage in the Mycosphaerellaceae in an unresolved position near Mycosphaerella microsora.
| S-EPMC3251325 | biostudies-literature
Project description:Morphological and molecular evidence strongly supported the monophyly of tribe Anemoneae DC.; however, phylogenetic relationships among genera of this tribe have still not been fully resolved. In this study, we sampled 120 specimens representing 82 taxa of tribe Anemoneae. One nuclear ribosomal internal transcribed spacer (nrITS) and six plastid markers (atpB-rbcL, matK, psbA-trnQ, rpoB-trnC, rbcL and rps16) were amplified and sequenced. Both Maximum likelihood and Bayesian inference methods were used to reconstruct phylogenies for this tribe. Individual datasets supported all traditional genera as monophyletic, except Anemone and Clematis that were polyphyletic and paraphyletic, respectively, and revealed that the seven single-gene datasets can be split into two groups, i.e. nrITS + atpB-rbcL and the remaining five plastid markers. The combined nrITS + atpB-rbcL dataset recovered monophyly of subtribes Anemoninae (i.e. Anemone s.l.) and Clematidinae (including Anemoclema), respectively. However, the concatenated plastid dataset showed that one group of subtribes Anemoninae (Hepatica and Anemone spp. from subgenus Anemonidium) close to the clade Clematis s.l. + Anemoclema. Our results strongly supported a close relationship between Anemoclema and Clematis s.l., which included Archiclematis and Naravelia. Non-monophyly of Anemone s.l. using the plastid dataset indicates to revise as two genera, new Anemone s.l. (including Pulsatilla, Barneoudia, Oreithales and Knowltonia), Hepatica (corresponding to Anemone subgenus Anemonidium).
| S-EPMC5376084 | biostudies-literature
Project description:Splitting of the genus Penaeus sensu lato into six new genera based on morphological features alone has been controversial in penaeid shrimp taxonomy. Several studies focused on building phylogenetic relations among the genera of Penaeus sensu lato. However, they lack in utilizing full mitochondrial DNA genome of shrimp representing all the six controversial genera. For the first time, the present study targeted the testing of all the six genera of Penaeus sensu lato for phylogenetic relations utilizing complete mitochondrial genome sequence. In addition, the study reports for the first time about the complete mitochondrial DNA genome sequence of Fenneropenaeus indicus, an important candidate species in aquaculture and fisheries, and utilized it for phylogenomics. The maximum likelihood and Bayesian approaches were deployed to generate and comprehend the phylogenetic relationship among the shrimp in the suborder, Dendrobranchiata. The phylogenetic relations established with limited taxon sampling considered in the study pointed to the monophyly of Penaeus sensu lato and suggested collapsing of the new genera to a single genus. Further, trends in mitogenome-wide estimates of average amino acid identity in the order Decapoda and the genus Penaeus sensu lato supported restoration of the old genus, Penaeus, rather promoting the creation of new genera.
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Project description:The postcranial anatomy of Crocodyliformes has historically been neglected, as most descriptions are based solely on skulls. Yet, the significance of the postcranium in crocodyliforms evolution is reflected in the great lifestyle diversity exhibited by the group, with members ranging from terrestrial animals to semi-aquatic and fully marine forms. Recently, studies have emphasized the importance of the postcranium. Following this trend, here we present a detailed description of the postcranial elements of Pissarrachampsa sera (Mesoeucrocodylia, Baurusuchidae), from the Adamantina Formation (Bauru Group, Late Cretaceous of Brazil). The preserved elements include dorsal vertebrae, partial forelimb, pelvic girdle, and hindlimbs. Comparisons with the postcranial anatomy of baurusuchids and other crocodyliforms, together with body-size and mass estimates, lead to a better understanding of the paleobiology of Pissarrachampsa sera, including its terrestrial lifestyle and its role as a top predator. Furthermore, the complete absence of osteoderms in P. sera, a condition previously known only in marine crocodyliforms, suggests osteoderms very likely played a minor role in locomotion of baurusuchids, unlike other groups of terrestrial crocodyliforms. Finally, a phylogenetic analysis including the newly recognized postcranial features was carried out, and exploratory analyses were performed to investigate the influence of both cranial and postcranial characters in the phylogeny of Crocodyliformes. Our results suggest that crocodyliform relationships are mainly determined by cranial characters. However, this seems to be a consequence of the great number of missing entries in the data set with only postcranial characters and not of the lack of potential (or synapomorphies) for this kind of data to reflect the evolutionary history of Crocodyliformes.
| S-EPMC4888301 | biostudies-literature
Project description:Three plastid regions, matK, rpl32-trnL and rpl16 intron and the ITS1-5.8S-ITS2 nuclear ribosomal DNA were used to demonstrate a phylogenetic placement of the genus Hederorkis (Orchidaceae) for the first time. The taxonomic position of this genus has been unclear thus far. The phylogenetic and morphological relations of Hederorkis to the most closely related genera Sirhookera, Adrorhizon, Bromheadia and Polystachya are also discussed. A hypothesis concerning an origin and evolution of Hederorkis is proposed. Hederorkis is an epiphytic two-leaved orchid genus with lateral inflorescence, non-resupinate flowers, elongate gynostemium and rudimentary column foot. It is native to the Indian Ocean Islands. Two species of Hederorkis are recognized worldwide, H. scandens endemic to Mauritius and Réunion and H. seychellensis endemic to Seychelles. For each of the species treated a full synonymy, detailed description and illustration are included. The distribution map and dichotomous keys to the species have also been provided.
| S-EPMC4406746 | biostudies-literature
Project description:MotivationIn most metagenomic sequencing studies, the initial analysis step consists in assessing the evolutionary provenance of the sequences. Phylogenetic (or Evolutionary) Placement methods can be employed to determine the evolutionary position of sequences with respect to a given reference phylogeny. These placement methods do however face certain limitations: The manual selection of reference sequences is labor-intensive; the computational effort to infer reference phylogenies is substantially larger than for methods that rely on sequence similarity; the number of taxa in the reference phylogeny should be small enough to allow for visually inspecting the results.ResultsWe present algorithms to overcome the above limitations. First, we introduce a method to automatically construct representative sequences from databases to infer reference phylogenies. Second, we present an approach for conducting large-scale phylogenetic placements on nested phylogenies. Third, we describe a preprocessing pipeline that allows for handling huge sequence datasets. Our experiments on empirical data show that our methods substantially accelerate the workflow and yield highly accurate placement results.Availability and implementationFreely available under GPLv3 at http://github.com/lczech/gappa.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC6449752 | biostudies-literature