Phylogeny and reclassification of Carpophilinae (Coleoptera: Nitidulidae), with insights into the origins of anthophily

2020 ◽  
Vol 189 (4) ◽  
pp. 1359-1369
Author(s):  
Gareth S Powell ◽  
Andrew R Cline ◽  
Alexandra G Duffy ◽  
Jennifer M Zaspel
Keyword(s):  
Life Histories ◽  
Ecosystem Functions ◽  
Evolutionary Relationships ◽  
Ancestral State ◽  
Multiple Origins ◽  
The Family ◽  
Novel Method ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
High Support

Abstract The family Nitidulidae is known for its diverse life histories, with some species considered economically detrimental pests, while others perform critical ecosystem functions. Despite this, their evolutionary relationships still lack support and understanding. A robust phylogenetic hypothesis and revised taxonomic classification for this group, particularly the subfamily Carpophilinae, could help delineate key lineages for assessing the evolution of both beneficial and pestiferous traits. The most complete molecular phylogeny of Carpophilinae to date, based on 37 ingroup taxa, covering four of the six recognized genera, is presented. Six genetic loci were used (16S, 18S, 28S, COI, H3 and ITS2), providing a total of 3500 bp of data. These data were generated using a novel method discussed here: wide-seq. Wide-seq utilizes next-generation sequencing platforms to generate data for specific loci that overlap with traditional Sanger sequences for the group. Carpophilinae recover as a well-supported clade with respect to the outgroup taxa. The genera Nitops, Urophorus and Caplothorax stat. nov. recover as monophyletic with high support. Caplothorax is formally given generic rank with a redescription and diagnosis. Anthophilous behaviour is coded for all taxa and an ancestral state reconstruction is performed, predicting multiple origins of this behaviour within Carpophilinae.

scholarly journals Pindara revisited – evolution and generic limits in Helvellaceae

2019 ◽  
Vol 42 (1) ◽  
pp. 186-204 ◽  
Author(s):  
K. Hansen ◽  
T. Schumacher ◽  
I. Skrede ◽  
S. Huhtinen ◽  
X.-H. Wang
Keyword(s):  
New Genus ◽  
Sister Group ◽  
Evolutionary Relationships ◽  
Lsu Rdna ◽  
Ancestral State ◽  
Representative Sampling ◽  
Phenotypic Characters ◽  
Separate Genus ◽  
The Family ◽  
Molecular Characters

The Helvellaceae encompasses taxa that produce some of the most elaborate apothecial forms, as well as hypogeous ascomata, in the class Pezizomycetes (Ascomycota). While the circumscription of the Helvellaceae is clarified, evolutionary relationships and generic limits within the family are debatable. A robust phylogeny of the Helvellaceae, using an increased number of molecular characters from the LSU rDNA, RPB2 and EF-1α gene regions (4 299 bp) and a wide representative sampling, is presented here. Helvella s.lat. was shown to be polyphyletic, because Helvella aestivalis formed a distant monophyletic group with hypogeous species of Balsamia and Barssia. All other species of Helvella formed a large group with the enigmatic Pindara (/Helvella) terrestris nested within it. The ear-shaped Wynnella constitutes an independent lineage and is recognised with the earlier name Midotis. The clade of the hypogeous Balsamia and Barssia, and H. aestivalis is coherent in the three-gene phylogeny, and considering the lack of phenotypic characters to distinguish Barssia from Balsamia we combine species of Barssia, along with H. aestivalis, in Balsamia. The closed/tuberiform, sparassoid H. astieri is shown to be a synonym of H. lactea; it is merely an incidental folded form of the saddle-shaped H. lactea. Pindara is a sister group to a restricted Helvella, i.e., excluding the /leucomelaena lineage, on a notably long branch. We recognise Pindara as a separate genus and erect a new genus Dissingia for the /leucomelaena lineage, viz. H. confusa, H. crassitunicata, H. leucomelaena and H. oblongispora. Dissingia is supported by asci that arise from simple septa; all other species of Helvellaceae have asci that arise from croziers, with one exception being the /alpina-corium lineage of Helvella s. str. This suggests ascus development from croziers is the ancestral state for the Helvellaceae and that ascus development from simple septa has evolved at least twice in the family. Our phylogeny does not determine the evolutionary relationships within Helvella s.str., but it is most parsimonious to infer that the ancestor of the helvelloids produced subsessile or shortly stipitate, cup-shaped apothecia. This shape has been maintained in some lineages of Helvella s.str. The type species of Underwoodia, Underwoodia columnaris, is a sister lineage to the rest of the Helvellaceae.

scholarly journals Measuring Illumina Size Bias Using REcount: A Novel Method for Highly Accurate Quantification of Engineered Genetic Constructs

2018 ◽  
Author(s):  
Daryl M. Gohl ◽  
Aaron Becker ◽  
Darrell Johnson ◽  
Shea Anderson ◽  
Bradley Billstein ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Restriction Enzymes ◽  
Digital Pcr ◽  
Counting Method ◽  
Novel Method ◽  
Sequencing Platforms ◽  
Next Generation Sequencing Ngs ◽  
Genetic Constructs ◽  
Generation Sequencing ◽  
Accurate Quantification

AbstractQuantification of DNA sequence tags associated with engineered genetic constructs underlies many genomics measurements. Typically, such measurements are done using PCR to enrich sequence tags and add adapters, followed by next-generation sequencing (NGS). However, PCR amplification can introduce significant quantitative error into these measurements. Here we describe REcount, a novel PCR-free direct counting method for NGS-based quantification of engineered genetic constructs. By comparing measurements of defined plasmid pools to droplet digital PCR data, we demonstrate that this method is highly accurate and reproducible. We further demonstrate that the REcount approach is amenable to multiplexing through the use of orthogonal restriction enzymes. Finally, we use REcount to provide new insights into clustering biases due to molecule length across different Illumina sequencing platforms.

scholarly journals Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Ancestral State ◽  
Trait Evolution ◽  
Natural Classification ◽  
Multiple Loci ◽  
The Family ◽  
Phylogenetic Perspective ◽  
Taxonomic Framework ◽  
First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

scholarly journals A new lineage of mazaediate fungi in the Eurotiomycetes: Cryptocaliciomycetidae subclass. nov., based on the new species Cryptocalicium blascoi and the revision of the ascoma evolution

2021 ◽  
Vol 20 (7) ◽  
pp. 889-904
Author(s):  
M. Prieto ◽  
Javier Etayo ◽  
I. Olariaga
Keyword(s):  
New Species ◽  
Common Ancestor ◽  
External Surface ◽  
Evolutionary Relationships ◽  
New Order ◽  
Ancestral State ◽  
Multigene Phylogeny ◽  
State Reconstruction ◽  
Distinct Structure ◽  
Dark Violet

AbstractThe class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

Systematic evidence from gene duplication and regulation

1990 ◽  
Vol 3 (1) ◽  
pp. 145
Author(s):  
DJ Colgan
Keyword(s):  
Gene Duplication ◽  
Evolutionary History ◽  
Tandem Duplication ◽  
Fragment Length Polymorphism ◽  
Duplicate Genes ◽  
Polymorphism Analysis ◽  
Multiple Origins ◽  
The Family ◽  
History Of ◽  
Phylogenetic Hypotheses

This paper is a review of the use of information regarding the presence of duplicate genes and their regulation in systematics. The review concentrates on data derived from protein electrophoresis and restriction fragment length polymorphism analysis. The appearance of a duplication in a subset of a group of species implies that the members of the subset belong to the same clade. Suppression of the duplication may render this clade apparently paraphyletic, but may itself be informative of relations within the lineage through patterns of loss of expression in all, or some tissues, or through restrictions of the formation of functional heteropolymers in polymeric enzymes. Examples are given of studies which have used such information to establish phylogenetic hypotheses at the family level, to identify an auto- or allo-polyploid origin of polyploid species and to determine whether there have been single or multiple origins of such species. The likelihood of homoplasy in the patterns of appearance and regulation of duplicates depends on the molecular basis of the duplication. In particular, the contrast between the expected consequences of tandem duplication and the expression of pseudogenes emphasises the value of determining the mechanism of the original duplication. Many instances of sporadic gene duplication are now known, and polyploidisation is a common event in the evolutionary history of both plants and animals. So the opportunities to discover duplicationrelated characters will arise in many systematic studies. A program is presented to increase the chances that such useful information will be recognisable during the studies.

scholarly journals Inductive Synthesis for Probabilistic Programs Reaches New Horizons

2021 ◽  
pp. 191-209
Author(s):  
Roman Andriushchenko ◽  
Milan Češka ◽  
Sebastian Junges ◽  
Joost-Pieter Katoen
Keyword(s):  
Deductive Reasoning ◽  
Synthesis Process ◽  
Worst Case ◽  
New Horizons ◽  
The Family ◽  
Pruning Strategy ◽  
Finite State ◽  
Novel Method ◽  
Partially Observable ◽  
Probabilistic Programs

AbstractThis paper presents a novel method for the automated synthesis of probabilistic programs. The starting point is a program sketch representing a finite family of finite-state Markov chains with related but distinct topologies, and a reachability specification. The method builds on a novel inductive oracle that greedily generates counter-examples (CEs) for violating programs and uses them to prune the family. These CEs leverage the semantics of the family in the form of bounds on its best- and worst-case behaviour provided by a deductive oracle using an MDP abstraction. The method further monitors the performance of the synthesis and adaptively switches between inductive and deductive reasoning. Our experiments demonstrate that the novel CE construction provides a significantly faster and more effective pruning strategy leading to an accelerated synthesis process on a wide range of benchmarks. For challenging problems, such as the synthesis of decentralized partially-observable controllers, we reduce the run-time from a day to minutes.

scholarly journals Multiple origins of insular woodiness on the Canary Islands are consistent with palaeoclimatic aridification

2020 ◽  
Author(s):  
Alexander Hooft van Huysduynen ◽  
Steven Janssens ◽  
Vincent Merckx ◽  
Rutger Vos ◽  
Luis Valente ◽  
...  
Keyword(s):  
Canary Islands ◽  
Canary Island ◽  
Distribution Patterns ◽  
Evolutionary Transition ◽  
North African ◽  
Island Species ◽  
Chloroplast Markers ◽  
Multiple Origins ◽  
The Family ◽  
Family Level

ABSTRACTAimInsular woodiness, referring to the evolutionary transition from herbaceousness towards woodiness on islands, has arisen at least 38 times on the Canary Islands. Distribution patterns and physiological experiments have suggested a link between insular woodiness and increased drought stress resistance in current-day species, but we do not know in which palaeoclimatic conditions these insular woody lineages originated. Therefore, we estimated the timing of colonisation events and origin of woodiness of multiple Canary Island lineages and reviewed the palaeoclimate based on literature.LocationCanary Islands (Spain).Taxon37 lineages, including 24 insular woody and 13 non-insular woody (i.e. herbaceous, ancestrally woody, and derived woody).MethodsTo enable a simultaneous dating analysis for all 37 lineages, two chloroplast markers (matK and rbcL) for 135 Canary Island species and 103 closely related continental relatives were sequenced and aligned to an existing matK-rbcL dataset including ca 24,000 species that was calibrated with 42 fossils from outside the Canaries. After constraining the species to the family level, 200 RAxML runs were performed and dated with TreePL.ResultsWoodiness in 80-90% of the insular woody lineages originated within the last 7 Myr, coinciding with the onset of major aridification events nearby the Canaries (start of north African desertification, followed by Messinian salinity crisis); in ca 55-65% of the insular woody lineages studied, woodiness developed within the last 3.2 Myr during which Mediterranean seasonality (yearly summer droughts) became established on the Canaries, followed by dry Pleistocene glacial fluctuations.Main conclusionsAlthough details of the initial colonisation and settlement of many island plant lineages remain elusive, our results are consistent with palaeodrought as a potential driver for woodiness in most of the insular woody Canary Island lineages studied.

Bidder's organs: Bufonid by-products of the evolutionary loss of hyperfecundity

1990 ◽  
Vol 11 (3) ◽  
pp. 225-235 ◽  
Author(s):  
Martha K. P. Roessler ◽  
Hobart M. Smith ◽  
David Chiszar
Keyword(s):  
Fat Body ◽  
Ancestral State ◽  
Male And Female ◽  
Functional Transition ◽  
The Family ◽  
Vestigial Structures ◽  
By Products ◽  
Transitory State

AbstractBidder's organs in both male and female bufonids are hypothesized to represent a transitory state in an evolutionary transformation from extensive, hyperfecund ovaries to smaller, less fecund ones-a transformation that other families of anurans experienced in forms now long extinct. Some members of the genus Bufo retain considerable hyperfecundity, but in derived species of Bufo and genera of Bufonidae a spectrum of ovarian reduction exists. In those groups, Bidder's organs normally persist, always in males and often in females, as an undifferentiated ovaroid or ovary in a non-functional transition between the ancestral state and modification as part of the fat body. The organs are gynomorphs in males and highly variable as vestigial structures, but may well have endocrinogenic functions in both sexes although gametogenic functions in nature have been lost in males. Presence of Bidder's organs is a derived condition in the context of anurans as a whole, but primitive within the family Bufonidae.

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