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 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.

scholarly journals Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

2005 ◽  
Vol 272 (1572) ◽  
pp. 1577-1586 ◽  
Author(s):  
Niklas Wahlberg ◽  
Michael F Braby ◽  
Andrew V.Z Brower ◽  
Rienk de Jong ◽  
Ming-Min Lee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Synergistic Effects ◽  
Strong Support ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Data Matrix ◽  
Morphological Data ◽  
Combined Analysis

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions ( COI , EF-1α and wingless ). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1α data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea.

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 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.

App2Vec: Context-Aware Application Usage Prediction

2021 ◽  
Vol 15 (6) ◽  
pp. 1-21
Author(s):  
Huandong Wang ◽  
Yong Li ◽  
Mu Du ◽  
Zhenhui Li ◽  
Depeng Jin
Keyword(s):  
Dirichlet Process ◽  
Service Providers ◽  
State Of The Art ◽  
Representation Learning ◽  
Context Aware ◽  
Challenging Problem ◽  
Performance Gap ◽  
Bayesian Mixture Model ◽  
Bayesian Mixture ◽  
Spatio Temporal

Both app developers and service providers have strong motivations to understand when and where certain apps are used by users. However, it has been a challenging problem due to the highly skewed and noisy app usage data. Moreover, apps are regarded as independent items in existing studies, which fail to capture the hidden semantics in app usage traces. In this article, we propose App2Vec, a powerful representation learning model to learn the semantic embedding of apps with the consideration of spatio-temporal context. Based on the obtained semantic embeddings, we develop a probabilistic model based on the Bayesian mixture model and Dirichlet process to capture when , where , and what semantics of apps are used to predict the future usage. We evaluate our model using two different app usage datasets, which involve over 1.7 million users and 2,000+ apps. Evaluation results show that our proposed App2Vec algorithm outperforms the state-of-the-art algorithms in app usage prediction with a performance gap of over 17.0%.

scholarly journals On a remarkable new species of <i>Tharsis</i>, a Late Jurassic teleostean fish from southern Germany: its morphology and phylogenetic relationships

Fossil Record ◽  
2019 ◽  
Vol 22 (1) ◽  
pp. 1-23 ◽  
Author(s):  
Gloria Arratia ◽  
Hans-Peter Schultze ◽  
Helmut Tischlinger
Keyword(s):  
New Species ◽  
Late Jurassic ◽  
Strong Support ◽  
Sister Group ◽  
Common Species ◽  
Upper Jurassic ◽  
Morphological Characters ◽  
Morphological Description ◽  
Sister Group Relationship ◽  
Southern Germany

Abstract. A complete morphological description, as preservation permits, is provided for a new Late Jurassic fish species (Tharsis elleri) together with a revision and comparison of some morphological features of Tharsis dubius, one of the most common species from the Solnhofen limestone, southern Germany. An emended diagnosis of the genus Tharsis – now including two species – is presented. The new species is characterized by a combination of morphological characters, such as the presence of a complete sclerotic ring formed by two bones placed anterior and posterior to the eye, a moderately short lower jaw with quadrate-mandibular articulation below the anterior half of the orbit, caudal vertebrae with neural and haemal arches fused to their respective vertebral centrum, and parapophyses fused to their respective centrum. A phylogenetic analysis based on 198 characters and 43 taxa is performed. Following the phylogenetic hypothesis, the sister-group relationship Ascalaboidae plus more advanced teleosts stands above the node of Leptolepis coryphaenoides. Both nodes have strong support among teleosts. The results confirm the inclusion of Ascalabos, Ebertichthys and Tharsis as members of this extinct family. Tharsis elleri n. sp. (LSID urn:lsid:zoobank.org:act:6434E6F5-2DDD-48CF-A2B1-827495FE46E6, date: 13 December 2018) is so far restricted to one Upper Jurassic German locality – Wegscheid Quarry near Schernfeld, Eichstätt – whereas Tharsis dubius is known not only from Wegscheid Quarry, but also from different localities in the Upper Jurassic of Bavaria, Germany, and Cerin in France.

scholarly journals Placozoa and Cnidaria are sister taxa

2017 ◽  
Author(s):  
Christopher E. Laumer ◽  
Harald Gruber-Vodicka ◽  
Michael G. Hadfield ◽  
Vicki B. Pearse ◽  
Ana Riesgo ◽  
...  
Keyword(s):  
Strong Support ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Large Dataset ◽  
Animal Evolution ◽  
Phylogenetic Placement ◽  
The Matrix ◽  
Show Evidence ◽  
Animal Phylogeny ◽  
Reduced Forms

AbstractThe phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria (=Planulozoa), also seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that the support for Planulozoa can be assigned to this source of systematic error. In interpreting this placozoan-cnidarian clade, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.

Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Peter J. Prentis ◽  
Hardeep S. Rai ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Special Issue ◽  
Likelihood Methods ◽  
The Family ◽  
Selection Of

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.

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