scholarly journals Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data

2019 ◽  
Vol 20 (5) ◽  
pp. 1072 ◽  
Author(s):  
Yuyu Wang ◽  
Xiaofan Zhou ◽  
Liming Wang ◽  
Xingyue Liu ◽  
Ding Yang ◽  
...  
Keyword(s):  
Large Scale ◽  
Gene Selection ◽  
Homogeneous Model ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Data Matrix ◽  
Bootstrap Support ◽  
Heterogeneous Model ◽  
Phylogenomic Analyses ◽  
A Site

Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.

scholarly journals Low-Coverage Whole Genomes Reveal the Higher Phylogeny of Green Lacewings

Insects ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 857
Author(s):  
Yuyu Wang ◽  
Ruyue Zhang ◽  
Yunlong Ma ◽  
Jing Li ◽  
Fan Fan ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Sister Group ◽  
Data Matrix ◽  
Limited Sampling ◽  
Green Lacewings ◽  
Whole Genomes ◽  
History Of ◽  
Low Coverage ◽  
Cretaceous Period

Green lacewings are one of the largest families within Neuroptera and are widely distributed all over the world. Many species within this group are important natural predators that are widely used for the biological control of pests in agricultural ecosystems. Several proposed phylogenetic relationships among the three subfamilies of Chrysopidae have been extensively debated. To further understand the higher phylogeny as well as the evolutionary history of Chrysopidae, we newly sequenced and analyzed the low-coverage genomes of 5 species (Apochrysa matsumurae, Chrysopa pallens, Chrysoperla furcifera, Italochrysa pardalina, Nothochrysa sinica), representing 3 subfamilies of Chrysopidae. There are 2213 orthologs selected to reconstruct the phylogenetic tree. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches, based on different data matrices. All the results suggested that Chrysopinae were a monophyletic sister group to the branch Apochrysinae + Nothochrysinae. These results were completely supported, except by the concatenation analyses of the nt data matrix, which suggested that Apochrysinae were a sister group to Chrysopinae + Nothchrysinae. The different topology from the nt data matrix may have been caused by the limited sampling of Chrysopidae. The divergence time showed that Chrysopinae diverged from Apochrysinae + Nothochrysinae during the Early Cretaceous period (144–151 Ma), while Aporchrysinae diverged from Nothochrysinae around 117–133 Ma. These results will improve our understanding of the higher phylogeny of Chrysopidae and lay a foundation for the utilization of natural predators.

Crustaceans and Insect Origins

2020 ◽  
pp. 105-120
Author(s):  
Björn M. von Reumont ◽  
Gregory D. Edgecombe
Keyword(s):  
Analytical Methods ◽  
Large Scale ◽  
Molecular Phylogenetics ◽  
Sister Group ◽  
Typical Pattern ◽  
Molecular Analyses ◽  
The Past ◽  
History Of ◽  
Critical Interpretation ◽  
Phylogenomic Analyses

Although Crustacea has a long history of being recognized as a formal taxonomic group in arthropod classification, the past 30 years have witnessed repeated challenges to crustacean monophyly. Few unambiguous autapomorphic characters for crustaceans have been proposed by morphologists, and many diagnostic characters can be interpreted as symplesiomorphies of Mandibulata. More serious challenges arise from molecular phylogenetics: irrespective of the scope of taxonomic and/or character sampling or analytical methods, a pancrustacean clade in which “Crustacea” is paraphyletic with respect to Hexapoda is retrieved. However, most traditional single to multigene studies infer phylogenies that display considerable mutual conflict. Although hexapod monophyly is robust and its deep branchings have recently been recovered using large-scale transcriptomic datasets, its crustacean sister group has been contentious. To some extent, a conclusive result is still hindered by uneven taxonomic coverage, with some key groups still being undersampled in phylogenomic studies. Nonetheless, phylogenomic analyses provide some robust results: notably, Hexapoda is part of a pancrustacean clade named Allotriocarida, which includes Cephalocarida and Branchiopoda as a grade or each other’s sister group, and Remipedia as the closest relatives to Hexapoda. Neuroanatomical support for a rival malacostracan-remipede-hexapod clade is incongruent with molecular datasets, which instead group Malacostraca, Copepoda, and Cirripedia as a clade. However, cirripedes resolve either as a sister group to copepods or to malacostracans, and this instability casts doubt on the typical pattern in molecular analyses that position malacostracans unexpectedly deep within the crustacean lineage. Pancrustacean phylogeny requires critical interpretation of phylogenomic data to reveal conflict in the data and ambiguous signals within the selected set of orthologous genes.

scholarly journals Using mitochondrial genomes to infer phylogenetic relationships among the oldest extant winged insects (Palaeoptera)

2017 ◽  
Author(s):  
Sereina Rutschmann ◽  
Ping Chen ◽  
Changfa Zhou ◽  
Michael T. Monaghan
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Data Matrix ◽  
Mitochondrial Genomes ◽  
Sampling Effort ◽  
Reconstruction Method ◽  
Marker Selection ◽  
Phylogenetic Resolution

AbstractPhylogenetic relationships among the basal orders of winged insects remain unclear, in particular the relationship of the Ephemeroptera (mayflies) and the Odonata (dragonflies and damselflies) with the Neoptera. Insect evolution is thought to have followed rapid divergence in the distant past and phylogenetic reconstruction may therefore be susceptible to problems of taxon sampling, choice of outgroup, marker selection, and tree reconstruction method. Here we newly sequenced three mitochondrial genomes representing the two most diverse families of the Ephemeroptera, one of which is a basal lineage of the order. We then used an additional 90 insect mitochondrial genomes to reconstruct their phylogeny using Bayesian and maximum likelihood approaches. Bayesian analysis supported a basal Odonata hypothesis, with Ephemeroptera as sister group to the remaining insects. This was only supported when using an optimized data matrix from which rogue taxa and terminals affected by long-branch attraction were removed. None of our analyses supported a basal Ephemeroptera hypothesis or Ephemeroptera + Odonata as monophyletic clade sister to other insects (i.e., the Palaeoptera hypothesis). Our newly sequenced mitochondrial genomes of Baetis rutilocylindratus, Cloeon dipterum, and Habrophlebiodes zijinensis had a complete set of protein coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Increased mayfly sampling, removal of problematic taxa, and a Bayesian phylogenetic framework were needed to infer phylogenetic relationships within the three ancient insect lineages of Odonata, Ephemeroptera, and Neoptera. Pruning of rogue taxa improved the number of supported nodes in all phylogenetic trees. Our results add to previous evidence for the Odonata hypothesis and indicate that the phylogenetic resolution of the basal insects can be resolved with more data and sampling effort.

scholarly journals The phylogeny and taxonomic status of the Chlorocystini (sensu stricto) (Homoptera, Tibicinidae)

1995 ◽  
Vol 65 (4) ◽  
pp. 201-231 ◽  
Author(s):  
A.J. de Boer
Keyword(s):  
Computer Program ◽  
Computer Analysis ◽  
Phylogenetic Reconstruction ◽  
Taxonomic Status ◽  
Sister Group ◽  
Sensu Stricto ◽  
Complete Data ◽  
Data Matrix ◽  
A Posteriori

The “Baeturia and related genera complex”, as defined earlier (De Boer, 1990) by shared aedeagal characters, is identified as the tribe Chlorocystini (sensu stricto). The Prasiini (sensu stricto) are identified as the sister group of the Chlorocystini (sensu stricto), while the genus Muda is recognized as the nearest outgroup. The phylogeny and biogeography of the sister group and outgroup is briefly discussed. Baeturia kuroiwae Matsumura is transferred to the genus Muda. A phylogenetic reconstruction of all 147 species of the Chlorocystini (sensu stricto) is presented, based on 154 characters and 409 character states. The computer program PAUP 3.1.1 (Swofford, 1993) was used for analysing the data; the genera Prasia and Muda were used as outgroups in this analysis. The results obtained from the computer analysis were slightly modified a posteriori, favouring some presumably phylogenetically important characters over strongly fluctuating ones. These final modifications were carried out with the aid of the computer program MacClade 3.0 (Maddison & Maddison, 1992). A complete data matrix and a list of characters and character states are given in an appendix; for descriptions and illustrations of these characters one is referred to previous publications.

scholarly journals Phylogenomics and the evolution of hemipteroid insects

2018 ◽  
Vol 115 (50) ◽  
pp. 12775-12780 ◽  
Author(s):  
Kevin P. Johnson ◽  
Christopher H. Dietrich ◽  
Frank Friedrich ◽  
Rolf G. Beutel ◽  
Benjamin Wipfler ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Single Copy ◽  
Molecular Dating ◽  
Protein Coding ◽  
Fossil Calibration ◽  
Large Scale Analysis ◽  
Phylogenetic Framework ◽  
Phylogenomic Analyses

Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.

scholarly journals Error, signal, and the placement of Ctenophora sister to all other animals

2015 ◽  
Vol 112 (18) ◽  
pp. 5773-5778 ◽  
Author(s):  
Nathan V. Whelan ◽  
Kevin M. Kocot ◽  
Leonid L. Moroz ◽  
Kenneth M. Halanych
Keyword(s):  
Systematic Error ◽  
Complex Traits ◽  
Data Partitioning ◽  
Compositional Bias ◽  
Ribosomal Protein Genes ◽  
Animal Evolution ◽  
Heterogeneous Model ◽  
Phylogenomic Analyses ◽  
A Site ◽  
Early Metazoan

Elucidating relationships among early animal lineages has been difficult, and recent phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the traditional view of Porifera as the earliest-branching animal lineage. To date, phylogenetic support for either ctenophores or sponges as sister to other animals has been limited and inconsistent among studies. Lack of agreement among phylogenomic analyses using different data and methods obscures how complex traits, such as epithelia, neurons, and muscles evolved. A consensus view of animal evolution will not be accepted until datasets and methods converge on a single hypothesis of early metazoan relationships and putative sources of systematic error (e.g., long-branch attraction, compositional bias, poor model choice) are assessed. Here, we investigate possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systematic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model. We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister. Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out. Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.

scholarly journals Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach

2016 ◽  
Vol 283 (1833) ◽  
pp. 20160857 ◽  
Author(s):  
Sarah Lemer ◽  
Vanessa L. González ◽  
Rüdiger Bieler ◽  
Gonzalo Giribet
Keyword(s):  
Phylogenetic Reconstruction ◽  
Strong Support ◽  
Sister Group ◽  
Data Matrix ◽  
Shell Microstructure ◽  
Bayesian Mixture Model ◽  
Bayesian Mixture ◽  
Exact Position ◽  
Adaptive Radiations ◽  
Basal Position

Mussels (Mytilida) are a group of bivalves with ancient origins and some of the most important commercial shellfish worldwide. Mytilida consists of approximately 400 species found in various littoral and deep-sea environments, and are part of the higher clade Pteriomorphia, but their exact position within the group has been unstable. The multiple adaptive radiations that occurred within Pteriomorphia have rendered phylogenetic classifications difficult and uncertainty remains regarding the relationships among most families. To address this phylogenetic uncertainty, novel transcriptomic data were generated to include all five orders of Pteriomorphia. Our results, derived from complex analyses of large datasets from 41 transcriptomes and evaluating possible pitfalls affecting phylogenetic reconstruction (matrix occupancy, heterogeneity, evolutionary rates, evolutionary models), consistently recover a well-supported phylogeny of Pteriomorphia, with the only exception of the most complete but smallest data matrix ( Matrix 3 : 51 genes, 90% gene occupancy). Maximum-likelihood and Bayesian mixture model analyses retrieve strong support for: (i) the monophyly of Pteriomorphia, (ii) Mytilida as a sister group to Ostreida, and (iii) Arcida as sister group to all other pteriomorphians. The basal position of Arcida is congruent with its shell microstructure (solely composed of aragonitic crystals), whereas Mytilida and Ostreida display a combination of a calcitic outer layer with an aragonitic inner layer composed of nacre tablets, the latter being secondarily lost in Ostreoidea.

scholarly journals Phylogeography in an “oyster” shell provides first insights into the genetic structure of an extinct Ostrea edulis population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sarah Hayer ◽  
Dirk Brandis ◽  
Alexander Immel ◽  
Julian Susat ◽  
Montserrat Torres-Oliva ◽  
...  
Keyword(s):  
Large Scale ◽  
Wadden Sea ◽  
Atlantic Coast ◽  
Phylogenetic Reconstruction ◽  
Oyster Shell ◽  
Glacial Refugia ◽  
Late Nineteenth Century ◽  
Ostrea Edulis ◽  
Geographic Ranges ◽  
The North

AbstractThe historical phylogeography of Ostrea edulis was successfully depicted in its native range for the first time using ancient DNA methods on dry shells from museum collections. This research reconstructed the historical population structure of the European flat oyster across Europe in the 1870s—including the now extinct population in the Wadden Sea. In total, four haplogroups were identified with one haplogroup having a patchy distribution from the North Sea to the Atlantic coast of France. This irregular distribution could be the result of translocations. The other three haplogroups are restricted to narrow geographic ranges, which may indicate adaptation to local environmental conditions or geographical barriers to gene flow. The phylogenetic reconstruction of the four haplogroups suggests the signatures of glacial refugia and postglacial expansion. The comparison with present-day O. edulis populations revealed a temporally stable population genetic pattern over the past 150 years despite large-scale translocations. This historical phylogeographic reconstruction was able to discover an autochthonous population in the German and Danish Wadden Sea in the late nineteenth century, where O. edulis is extinct today. The genetic distinctiveness of a now-extinct population hints at a connection between the genetic background of O. edulis in the Wadden Sea and for its absence until today.

scholarly journals Prevalence and genetic diversity of avian haemosporidian parasites in wild bird species of the order Columbiformes

2021 ◽  
Author(s):  
Yvonne R. Schumm ◽  
Dimitris Bakaloudis ◽  
Christos Barboutis ◽  
Jacopo G. Cecere ◽  
Cyril Eraud ◽  
...  
Keyword(s):  
Host Species ◽  
Large Scale ◽  
Phylogenetic Reconstruction ◽  
Bird Species ◽  
Avian Species ◽  
Blood Parasites ◽  
Migration Strategy ◽  
Haemosporidian Parasites ◽  
Multiplex Pcr Assay ◽  
And Migration

AbstractDiseases can play a role in species decline. Among them, haemosporidian parasites, vector-transmitted protozoan parasites, are known to constitute a risk for different avian species. However, the magnitude of haemosporidian infection in wild columbiform birds, including strongly decreasing European turtle doves, is largely unknown. We examined the prevalence and diversity of haemosporidian parasites Plasmodium, Leucocytozoon and subgenera Haemoproteus and Parahaemoproteus in six species of the order Columbiformes during breeding season and migration by applying nested PCR, one-step multiplex PCR assay and microscopy. We detected infections in 109 of the 259 screened individuals (42%), including 15 distinct haemosporidian mitochondrial cytochrome b lineages, representing five H. (Haemoproteus), two H. (Parahaemoproteus), five Leucocytozoon and three Plasmodium lineages. Five of these lineages have never been described before. We discriminated between single and mixed infections and determined host species-specific prevalence for each parasite genus. Observed differences among sampled host species are discussed with reference to behavioural characteristics, including nesting and migration strategy. Our results support previous suggestions that migratory birds have a higher prevalence and diversity of blood parasites than resident or short-distance migratory species. A phylogenetic reconstruction provided evidence for H. (Haemoproteus) as well as H. (Parahaemoproteus) infections in columbiform birds. Based on microscopic examination, we quantified parasitemia, indicating the probability of negative effects on the host. This study provides a large-scale baseline description of haemosporidian infections of wild birds belonging to the order Columbiformes sampled in the northern hemisphere. The results enable the monitoring of future changes in parasite transmission areas, distribution and diversity associated with global change, posing a potential risk for declining avian species as the European turtle dove.

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