Compositional phylogenomic modelling resolves the 'Zoraptera problem': Zoraptera are sister to all other polyneopteran insects

The evolution of wings propelled insects to their present mega-diversity. However, interordinal relationships of early-diverging winged insects and the timescale of their evolution are difficult to resolve, in part due to uncertainties in the placement of the enigmatic and species-poor order Zoraptera. The 'Zoraptera problem' has remained a contentious issue in insect evolution since its discovery more than a century ago. This is a key issue because different placements of Zoraptera imply dramatically different scenarios of diversification and character evolution among polyneopteran. Here, we investigate the systematic placement of Zoraptera using the largest protein-coding gene dataset available to date, deploying methods to mitigate common sources of error in phylogenomic inference, and testing historically proposed hypotheses of zorapteran evolution. We recover Zoraptera as the earliest-diverging polyneopteran order, while earwigs (Dermaptera) and stoneflies (Plecoptera) form a monophyletic clade (Dermoplectopterida) sister to the remainder of Polyneoptera. The morphology and palaeobiology of stem-zorapterans are informed by Mesozoic fossils. The gut content and mouthparts of a male specimen of Zorotypus nascimbenei from Kachin amber (Cretaceous) reveal a fungivorous diet of Mesozoic zorapterans, akin to extant species. Based on a set of 42 justified fossil and stratigraphic calibrations, we recover a Devonian origin of winged insects and Polyneoptera, suggesting that these groups coincided with the rise of arborescence during the diversification of early terrestrial plants, fungi, and animals. Our results provide a robust framework for understanding the pattern and timescale of early winged insect diversification.

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Evolutionary Relations of Hexanchiformes Deep-Sea Sharks Elucidated by Whole Mitochondrial Genome Sequences

BioMed Research International ◽

10.1155/2013/147064 ◽

2013 ◽

Vol 2013 ◽

pp. 1-11 ◽

Cited By ~ 10

Author(s):

Keiko Tanaka ◽

Takashi Shiina ◽

Taketeru Tomita ◽

Shingo Suzuki ◽

Kazuyoshi Hosomichi ◽

...

Keyword(s):

Genetic Relationships ◽

Close Relation ◽

Rrna Genes ◽

Gill Slit ◽

Mtdna Sequences ◽

Protein Coding ◽

Bayesian Phylogenetic Analysis ◽

Extant Species ◽

Complete Mitogenome ◽

Cartilaginous Fishes

Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA) sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes) species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi,Chlamydoselachus anguineus(frilled shark) is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved asChlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus,H. nakamurai))). Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks.

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Additions to Ochroconis from India

Phytotaxa ◽

10.11646/phytotaxa.427.3.2 ◽

2019 ◽

Vol 427 (3) ◽

pp. 186-199

Author(s):

ARCHANA SINGH ◽

NIKHIL KUMAR SINGH ◽

PARAS NATH SINGH ◽

RAGHVENDRA SINGH ◽

NAWAL KISHORE DUBEY

Keyword(s):

New Species ◽

Medicinal Plant ◽

Ribosomal Dna ◽

Leaf Surface ◽

Novel Species ◽

Phylogenetic Analyses ◽

Nuclear Ribosomal Dna ◽

Monophyletic Clade ◽

Protein Coding

Ochroconis helicteris, a novel species of the oligotrophic genus Ochroconis (Sympoventuriaceae, Venturiales), has been described and illustrated. Morphologically, this species has characters similar to allied species in the genus Ochroconis, but differs in conidial dimensions and shape. Phylogenetic analyses using nuclear ribosomal DNA gene ITS and protein coding gene BT2 revealed it clustering as monophyletic clade which was separated from known Ochroconis species. New species was isolated from leaf surface of medicinal plant Helicteris isora L.

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SYNOPSIS OF THE NEOTROPICAL GENUS OZAENA OLIVIER: CLASSIFICATION AND RECONSTRUCTED EVOLUTIONARY HISTORY (COLEOPTERA: CARABIDAE: OZAENINI)

The Canadian Entomologist ◽

10.4039/ent122779-9 ◽

1990 ◽

Vol 122 (5) ◽

pp. 779-815 ◽

Cited By ~ 3

Author(s):

George E. Ball ◽

Danny Shpeley

Keyword(s):

South America ◽

Sister Group ◽

Structural Features ◽

Character Evolution ◽

Type Locality ◽

Sister Taxon ◽

Fore Tibia ◽

Sensilla Basiconica ◽

Extant Species ◽

And Shifts

AbstractDescriptions and illustrations of structural features of adults, a key, and chorological data provide the basis for characterizing the genus Ozaena Olivier and classifying the 10 included species, two of which are new: O. maxi (type locality: Iracubo, CAYENNE), and O. manu (type locality: Manu National Park, Madre de Dios Province, PERU). With a geographical range that extends from ca. 30°S to 30°N in the New World, all species of Ozaena occur in cis-Andean South America, only two ranging farther north: O. dentipes Olivier, to Panama; and O. lemoulti Bänninger to southern Arizona, USA. A reconstructed phylogeny postulates the following: the genus Platycerozaena Bänninger as the sister-group of Ozaena, together these genera comprising the Ozaena genus-group; within Ozaena, the O. dentipes group as sister-taxon of the O. lemoulti + convexa groups; within the O. dentipes group, O. maxi as sister-taxon of O. linearis Bänninger + dentipes; within the O. lemoulti group, the sequence O. ecuadorica Bänn. (O. elavata Bänn. [O. lemoulti + martinezi Ogueta]); and within the O. convexa group, O. grossa Bänn. as sister-taxon of O. convexa Bänn. + manu. Character evolution involves losses, gains, and shifts, in about equal numbers. Convergence is relatively rare, involving only three of 35 characters. The predominant mode of character evolution is simple, with few examples of sequential changes sustained through several speciation events. Basic modifications in evolution of the ground-plan of the Ozaena genus-group include reduction or loss (for example, tactile sense organs, antennal cleaner of the fore tibia, and adhesive vestiture of the male fore tarsi), and enhancement or gain (for example, scale-like sensilla basiconica on pronotum and elytra, concentration of sensilla basiconica in groups on the antennomeres, particularly antennomere 11). Within Ozaena, many modifications to the antennae and mouthparts indicate the importance of these organs to evolution of the group.Based on phylogenetic relationships and the distribution pattern of the extant species, a reconstructed geographical history of Ozaena postulates the following: first, a vicariance event in South America separating the ancestral stock of Ozaena into a northern vicar that gave rise to the O. dentipes group, and a southern vicar that gave rise to the O. lemoulti and convexa groups; followed by cycles of range expansion and contraction that allowed for differentiation of successive stocks of species. The temporal range for these speciation events is estimated to extend over a period of about 12 million years, or from the latter part of the Miocene epoch to the Recent. The most recent speciation events are estimated to be of Pliocene age.Based on lack of differentiation of South American and Middle American representatives of O. dentipes and O. lemoulti respectively, and extent of range in Middle America, these two species are postulated to be relatively recent invaders of the latter area, with O. dentipes being the more recent to arrive.

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Phenotypic disparity and adaptive radiation in the genus Cladia (Lecanorales, Ascomycota)

Australian Systematic Botany ◽

10.1071/sb10010 ◽

2010 ◽

Vol 23 (4) ◽

pp. 239 ◽

Cited By ~ 19

Author(s):

H. Thorsten Lumbsch ◽

Sittiporn Parnmen ◽

Achariya Rangsiruji ◽

John A. Elix

Keyword(s):

Dna Sequences ◽

Adaptive Radiation ◽

Alternative Hypothesis ◽

Long Distance ◽

Broad Distribution ◽

Bayesian Analyses ◽

Protein Coding ◽

Morphological Disparity ◽

Extant Species ◽

Nuclear Its

Phylogenetic relationships of the genera Cladia, Heterodea and Ramalinora were reconstructed using a combined dataset of ribosomal nuclear ITS and LSU and mitochondrial SSU, and protein-coding Mcm7 DNA sequences. Maximum likelihood and Bayesian analyses strongly supported a monophyletic group in which the species of the foliose genus Heterodea and the crustose genus Ramalinora were nested within the fruticose genus Cladia. Alternative hypothesis testing rejected an independent status of Ramalinora. We tested the hypothesis that an adaptive radiation led to the morphological disparity found in the Cladia clade. Gamma-statistics indicated a significantly disproportional clustering of origins of extant lineages at the base of the Cladia clade and lineage-through-time plots were also consistent with the hypothesis of an adaptive radiation at the base of the Cladia clade. Ancestral-range reconstructions supported an origin of Cladia and the three major lineages within Cladia in Australia. On the basis of these results, we propose an evolutionary hypothesis for the genus. The results suggest that processes of adaptive radiation of the ancestor of Cladia in Australia led to the morphological disparity in the extant taxa, and that the broad distribution of some extant species is due to subsequent long-distance dispersal.

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A shift in aggregation avoidance strategy marks a long-term direction to protein evolution

10.1101/176867 ◽

2017 ◽

Cited By ~ 1

Author(s):

S.G. Foy ◽

B.A. Wilson ◽

J. Bertram ◽

M.H.J. Cordes ◽

J. Masel

Keyword(s):

Amino Acids ◽

Common Ancestor ◽

Gene Families ◽

Protein Coding ◽

Hydrophobic Residues ◽

Extant Species ◽

Aggregation Problem ◽

Hydrophobic Amino Acids ◽

Ancestral States

AbstractTo detect a direction to evolution, without the pitfalls of reconstructing ancestral states, we need to compare “more evolved” to “less evolved” entities. But because all extant species have the same common ancestor, none are chronologically more evolved than any other. However, different gene families were born at different times, allowing us to compare young protein-coding genes to those that are older and hence have been evolving for longer. To be retained during evolution, a protein must not only have a function, but must also avoid toxic dysfunction such as protein aggregation. There is conflict between the two requirements; hydrophobic amino acids form the cores of protein folds, but also promote aggregation. Young genes avoid strongly hydrophobic amino acids, which is presumably the simplest solution to the aggregation problem. Here we show that young genes’ few hydrophobic residues are clustered near one another along the primary sequence, presumably to assist folding. The higher aggregation risk created by the higher hydrophobicity of older genes is counteracted by more subtle effects in the ordering of the amino acids, including a reduction in the clustering of hydrophobic residues until they eventually become more interspersed than if distributed randomly. This interspersion has previously been reported to be a general property of proteins, but here we find that it is restricted to old genes. Quantitatively, the index of dispersion delineates a gradual trend, i.e. a decrease in the clustering of hydrophobic amino acids over billions of years.

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Morpho-Phylo Taxonomy of Novel Dothideomycetous Fungi Associated With Dead Woody Twigs in Yunnan Province, China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.654683 ◽

2021 ◽

Vol 12 ◽

Author(s):

Peter E. Mortimer ◽

Rajesh Jeewon ◽

Jian-Chu Xu ◽

Saisamorn Lumyong ◽

Dhanushka N. Wanasinghe

Keyword(s):

Yunnan Province ◽

Phylogenetic Analyses ◽

Protein Coding ◽

Research Attention ◽

Multiple Gene ◽

Asexual Morph ◽

Coding Regions ◽

Extant Species ◽

Ocular Chamber ◽

Taxonomic Novelties

Within the field of mycology, macrofungi have been relatively well-studied when compared to microfungi. However, the diversity and distribution of microfungi inhabiting woody material have not received the same degree of research attention, especially in relatively unexplored regions, such as Yunnan Province, China. To help address this knowledge gap, we collected and examined fungal specimens from different plants at various locations across Yunnan Province. Our investigation led to the discovery of four species that are clearly distinct from extant ones. These taxonomic novelties were recognized based on morphological comparisons coupled with phylogenetic analyses of multiple gene sequences (non-translated loci and protein-coding regions). The monotypic genus Neoheleiosa gen. nov. (type: N. lincangensis) is introduced in Monoblastiaceae (Monoblastiales) for a woody-based saprobic ascomycete that possesses globose to subglobose or obpyriform ascomata with centric or eccentric, papillate ostioles, an ascomatal wall with thin-walled cells of textura globulosa, cylindric, pedicellate asci with an ocular chamber, and 1-septate, brown, guttulate, longitudinally striated, bicellular ascospores. Neoheleiosa has a close phylogenetic affinity to Heleiosa, nevertheless, it is morphologically dissimilar by its peridium cells and ornamented ascospores. Acrocalymma hongheense and A. yuxiense are described and illustrated as new species in Acrocalymmaceae. Acrocalymma hongheense is introduced with sexual and asexual (coelomycetous) features. The sexual morph is characterized by globose to subglobose, ostiolate ascomata, a peridium with textura angularis cells, cylindric-clavate asci with a furcate to truncate pedicel and an ocular chamber, hyaline, fusiform, 1-septate ascospores which are surrounded by a thick, distinct sheath, and the asexual morph is featured by pycnidial conidiomata, subcylindrical, hyaline, smooth, annelledic, conidiogenous cells, hyaline, guttulate, subcylindrical, aseptate conidia with mucoid ooze at the apex and with a rounded hilum at the base. Acrocalymma yuxiense is phylogenetically distinct from other extant species of Acrocalymma and differs from other taxa in Acrocalymma in having conidia with three vertical eusepta. Magnibotryascoma kunmingense sp. nov. is accommodated in Teichosporaceae based on its coelomycetous asexual morph which is characterized by pycnidial, globose to subglobose, papillate conidiomata, enteroblastic, annelledic, discrete, cylindrical to oblong, hyaline conidiogenous cells arising from the inner layer of pycnidium wall, subglobose, oval, guttulate, pale brown and unicelled conidia.

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Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae)

Systematic Biology ◽

10.1093/sysbio/syab013 ◽

2021 ◽

Author(s):

Nicolas Nesi ◽

Georgia Tsagkogeorga ◽

Susan M Tsang ◽

Violaine Nicolas ◽

Aude Lalis ◽

...

Keyword(s):

Information Content ◽

Incomplete Lineage Sorting ◽

Gene Tree ◽

Fruit Bats ◽

Lineage Sorting ◽

Protein Coding ◽

Old World ◽

Nectar Feeding ◽

Extant Species ◽

Evolutionary Distinctiveness

Abstract The family Pteropodidae (Old World fruit bats) comprises $>$200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with $>$50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the main pteropodid lineages is essential if we are to fully understand their evolutionary distinctiveness, and the extent to which these bats have transitioned to nectar-feeding. Here we generated orthologous sequences for $>$1400 nuclear protein-coding genes (2.8 million base pairs) across 114 species from 43 genera of Old World fruit bats (57% and 96% of extant species- and genus-level diversity, respectively), and combined phylogenomic inference with filtering by information content to resolve systematic relationships among the major lineages. Concatenation and coalescent-based methods recovered three distinct backbone topologies that were not able to be reconciled by filtering via phylogenetic information content. Concordance analysis and gene genealogy interrogation show that one topology is consistently the best supported, and that observed phylogenetic conflicts arise from both gene tree error and deep incomplete lineage sorting. In addition to resolving long-standing inconsistencies in the reported relationships among major lineages, we show that Old World fruit bats have likely undergone at least seven independent dietary transitions from frugivory to nectarivory. Finally, we use this phylogeny to identify and describe one new genus. [Chiroptera; coalescence; concordance; incomplete lineage sorting; nectar feeder; species tree; target enrichment.]

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Complete mitogenome of Kashmir musk deer (Moschus cupreus) and its comparative phylogenetic relationships

10.1101/2020.08.25.265850 ◽

2020 ◽

Author(s):

Bhim Singh ◽

Kumudani Bala Gautam ◽

Subhashree Sahoo ◽

Ajit Kumar ◽

Sandeep Kumar Gupta

Keyword(s):

Ribosomal Rna ◽

Musk Deer ◽

Protein Coding ◽

Gc Skew ◽

Extant Species ◽

Complete Mitogenome ◽

Phylogeny And Evolution ◽

Coding Control ◽

Rna Genes ◽

Insight Into

AbstractThe endangered Kashmir musk deer (Moschus cupreus) is native to the high altitudinal region of the Himalayas. In this study, we sequenced, annotated and characterized the complete mitogenome of M. cupreus to gain insight into the molecular phylogeny and evolution of musk deer. The mitogenome of M. cupreus, which is 16,354 bp long comprised 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and non-coding control region. The M. cupreus mitogenome composition was highly A+T biased 68.42%, and exhibited a positive AT skew (0.082) and negative GC skew (0.307). The phylogenetic analysis suggested that KMD is the most primitive extant species in the genus Moschus whereas Alpine musk deer (M. chrysogaster) and Himalayan musk deer (M. leucogaster) are closely related. This result confirmed the placement of M. cupreus within the monotypic family Moschidae of musk deer. This study provides a better understanding of lineage identification and musk deer evolution for further research.

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Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii

BMC Genomics ◽

10.1186/s12864-021-08162-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Dawoon Chung ◽

Yong Min Kwon ◽

Youngik Yang

Keyword(s):

Rna Sequencing ◽

Draft Genome ◽

Sequencing Analysis ◽

Sequencing Data ◽

Terrestrial Plants ◽

Protein Coding ◽

Oxford Nanopore ◽

Wide Range ◽

The Family ◽

Encoding Genes

Abstract Background Trichoderma is a genus of fungi in the family Hypocreaceae and includes species known to produce enzymes with commercial use. They are largely found in soil and terrestrial plants. Recently, Trichoderma simmonsii isolated from decaying bark and decorticated wood was newly identified in the Harzianum clade of Trichoderma. Due to a wide range of applications in agriculture and other industries, genomes of at least 12 Trichoderma spp. have been studied. Moreover, antifungal and enzymatic activities have been extensively characterized in Trichoderma spp. However, the genomic information and bioactivities of T. simmonsii from a particular marine-derived isolate remain largely unknown. While we screened for asparaginase-producing fungi, we observed that T. simmonsii GH-Sj1 strain isolated from edible kelp produced asparaginase. In this study, we report a draft genome of T. simmonsii GH-Sj1 using Illumina and Oxford Nanopore technologies. Furthermore, to facilitate biotechnological applications of this species, RNA-sequencing was performed to elucidate the transcriptional profile of T. simmonsii GH-Sj1 in response to asparaginase-rich conditions. Results We generated ~ 14 Gb of sequencing data assembled in a ~ 40 Mb genome. The T. simmonsii GH-Sj1 genome consisted of seven telomere-to-telomere scaffolds with no sequencing gaps, where the N50 length was 6.4 Mb. The total number of protein-coding genes was 13,120, constituting ~ 99% of the genome. The genome harbored 176 tRNAs, which encode a full set of 20 amino acids. In addition, it had an rRNA repeat region consisting of seven repeats of the 18S-ITS1–5.8S-ITS2–26S cluster. The T. simmonsii genome also harbored 7 putative asparaginase-encoding genes with potential medical applications. Using RNA-sequencing analysis, we found that 3 genes among the 7 putative genes were significantly upregulated under asparaginase-rich conditions. Conclusions The genome and transcriptome of T. simmonsii GH-Sj1 established in the current work represent valuable resources for future comparative studies on fungal genomes and asparaginase production.

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Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny

Plants ◽

10.3390/plants9020199 ◽

2020 ◽

Vol 9 (2) ◽

pp. 199 ◽

Cited By ~ 1

Author(s):

Arif Khan ◽

Sajjad Asaf ◽

Abdul Latif Khan ◽

Tariq Shehzad ◽

Ahmed Al-Rawahi ◽

...

Keyword(s):

Inverted Repeat ◽

Sequence Variation ◽

Phylogenetic Analyses ◽

Single Copy ◽

Large Single Copy ◽

Monophyletic Clade ◽

Protein Coding ◽

The Family ◽

Generation Sequencing ◽

Large Single Copy Region

Euphorbia is one of the largest genera in the Euphorbiaceae family, comprising 2000 species possessing commercial, medicinal, and ornamental importance. However, there are very little data available on their molecular phylogeny and genomics, and uncertainties still exist at a taxonomic level. Herein, we sequence the complete chloroplast (cp) genomes of two species, E. larica and E. smithii, of the genus Euphorbia through next-generation sequencing and perform a comparative analysis with nine related genomes in the family. The results revealed that the cp genomes had similar quadripartite structure, gene content, and genome organization with previously reported genomes from the same family. The size of cp genomes ranged from 162,172 to 162,358 bp with 132 and 133 genes, 8 rRNAs, 39 tRNA in E. smithii and E. larica, respectively. The numbers of protein-coding genes were 85 and 86, with each containing 19 introns. The four-junction regions were studied and results reveal that rps19 was present at JLB (large single copy region and inverted repeat b junction) in E. larica where its complete presence was located in the IRb (inverted repeat b) region in E. smithii. The sequence comparison revealed that highly divergent regions in rpoC1, rpocB, ycf3, clpP, petD, ycf1, and ndhF of the cp genomes might provide better understanding of phylogenetic inferences in the Euphorbiaceae and order Malpighiales. Phylogenetic analyses of this study illustrate sister clades of E. smithii with E. tricullii and these species form a monophyletic clade with E. larica. The current study might help us to understand the genome architecture, genetic diversity among populations, and evolutionary depiction in the genera.

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