Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An ...accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e.g., RNA sequencing). Here, identification of orthologous nucleotide or amino acid sequences can be achieved using a graph-based approach that maps nucleotide sequences to genes of known orthology. Existing implementations of this approach, however, suffer from algorithmic issues that may cause problems in downstream analyses.
We present a new software pipeline, Orthograph, that addresses and solves the above problems and implements useful features for a wide range of comparative genomic and transcriptomic analyses. Orthograph applies a best reciprocal hit search strategy using profile hidden Markov models and maps nucleotide sequences to the globally best matching cluster of orthologous genes, thus enabling researchers to conveniently and reliably delineate orthologs and paralogs from transcriptomic and genomic sequence data. We demonstrate the performance of our approach on de novo-sequenced and assembled transcript libraries of 24 species of apoid wasps (Hymenoptera: Aculeata) as well as on published genomic datasets.
With Orthograph, we implemented a best reciprocal hit approach to reference-based orthology prediction for coding nucleotide sequences such as RNAseq data. Orthograph is flexible, easy to use, open source and freely available at https://mptrsen.github.io/Orthograph . Additionally, we release 24 de novo-sequenced and assembled transcript libraries of apoid wasp species.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of ...Neuropterida has been extensively studied, but no strong consensus exists concerning the phylogenetic relationships within the order Neuroptera. Here, we assembled a novel transcriptomic dataset to address previously unresolved issues in the phylogeny of Neuropterida and to infer divergence times within the group. We tested the robustness of our phylogenetic estimates by comparing summary coalescent and concatenation-based phylogenetic approaches and by employing different quartet-based measures of phylogenomic incongruence, combined with data permutations.
Our results suggest that the order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae is inferred as sister to all remaining neuropteran families suggesting that larval cryptonephry could be a ground plan feature of Neuroptera. A clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e. Osmyloidea) is inferred as sister to all other Neuroptera except Coniopterygidae, and Dilaridae is placed as sister to all remaining neuropteran families. Ithonidae is inferred as the sister group of monophyletic Myrmeleontiformia. The phylogenetic affinities of Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and quartet-based analyses showed only weak support for the placement of Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular dating analyses suggest that most families of Neuropterida started to diversify in the Jurassic and our ancestral character state reconstructions suggest a primarily terrestrial environment of the larvae of Neuropterida and Neuroptera.
Our extensive phylogenomic analyses consolidate several key aspects in the backbone phylogeny of Neuropterida, such as the basal placement of Coniopterygidae within Neuroptera and the monophyly of Osmyloidea. Furthermore, they provide new insights into the timing of diversification of Neuropterida. Despite the vast amount of analyzed molecular data, we found that certain nodes in the tree of Neuroptera are not robustly resolved. Therefore, we emphasize the importance of integrating the results of morphological analyses with those of sequence-based phylogenomics. We also suggest that comparative analyses of genomic meta-characters should be incorporated into future phylogenomic studies of Neuropterida.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The evolution of the coleopteran suborder Adephaga is discussed based on a robust phylogenetic background. Analyses of morphological characters yield results nearly identical to recent molecular ...phylogenies, with the highly specialized Gyrinidae placed as sister to the remaining families, which form two large, reciprocally monophyletic subunits, the aquatic Haliplidae + Dytiscoidea (Meruidae, Noteridae, Aspidytidae, Amphizoidae, Hygrobiidae, Dytiscidae) on one hand, and the terrestrial Geadephaga (Trachypachidae + Carabidae) on the other. The ancestral habitat of Adephaga, either terrestrial or aquatic, remains ambiguous. The former option would imply two or three independent invasions of aquatic habitats, with very different structural adaptations in larvae of Gyrinidae, Haliplidae and Dytiscoidea.
This study presents the largest set of morphological characters of adults and immature stages ever compiled for the coleopteran suborder Adephaga.
Analyses of the morphological characters yield results nearly identical to recent analyses of molecular data, suggesting that a stable phylogeny has been achieved.
The character transformation on the phenotypic level is reconstructed using a formal approach for the first time, based on the robust phylogenetic pattern and mesquite.
Phylogenomics and the evolution of hemipteroid insects Johnson, Kevin P.; Dietrich, Christopher H.; Friedrich, Frank ...
Proceedings of the National Academy of Sciences,
12/2018, Letnik:
115, Številka:
50
Journal Article
Recenzirano
Odprti dostop
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.
The clade Syndermata includes the endoparasitic Acanthocephala, the epibiotic Seisonidea, and the free-living Bdelloidea and Monogononta. The phylogeny of Syndermata is highly debated, hindering the ...understanding of the evolution of morphological features, reproductive modes, and lifestyles within the group. Here, we use publicly available whole-genome data to re-evaluate syndermatan phylogeny and assess the credibility of alternative hypotheses, using a new combination of phylogenomic methods. We found that the Hemirotifera and Pararotatoria hypotheses were recovered under combinations of datasets and methods with reduced possibility of systematic error in concatenation-based analyses. In contrast, the Seisonidea-sister and Lemniscea hypotheses were recovered under dataset combinations with increased possibility of systematic error. Hemirotifera was further supported by whole-genome microsynteny analyses and species-tree methods that use multi-copy orthogroups after removing distantly related outgroups. Pararotatoria was only partially supported by microsynteny-based phylogenomic reconstructions. Hence, Hemirotifera and partially Pararotatoria were supported by independent phylogenetic methods and data-evaluation approaches. These two hypotheses have important implications for the evolution of syndermatan morphological features, such as the gradual reduction of locomotory ciliation from the common ancestor of Syndermata in the stem lineage of Pararotatoria. Our study illustrates the importance of combining various types of evidence to resolve difficult phylogenetic questions.
The Syrphoidea (families Pipunculidae and Syrphidae) has been suggested to be the sister group of the Schizophora, the largest species radiation of true flies. A major challenge in dipterology is ...inferring the phylogenetic relationship between Syrphoidea and Schizophora in order to understand the evolutionary history of flies. Using newly sequenced transcriptomic data of Syrphidae, Pipunculidae and closely related lineages, we were able to fully resolve phylogenetic relationships of Syrphoidea using a supermatrix approach with more than 1 million amino acid positions derived from 3145 genes, including 19 taxa across nine families. Platypezoidea were inferred as a sister group to Eumuscomorpha, which was recovered monophyletic. While Syrphidae were also found to be monophyletic, the superfamily Syrphoidea was not recovered as a monophyletic group, as Pipunculidae were inferred as sister group to Schizophora. Within Syrphidae, the subfamily Microdontinae was resolved as sister group to the remaining taxa, Syrphinae and Pipizinae were placed as sister groups, and the monophyly of Eristalinae was not recovered. Although our results are consistent with previously established hypotheses on Eumuscomorphan evolution, our approach is new to dipteran phylogeny, using larger‐scale transcriptomic data for the first time for this insect group.
Nineteen de novo transcriptomes of nine dipteran families were analysed to test the monophyly of Syrphoidea (Syrphidae + Pipunculidae).
The final data matrix comprised more than 1 million amino acid positions derived from 3145 genes, the largest dataset for Diptera so far.
Pipunculidae was resolved as sister group to Schizophora, not grouped with Syrphidae. Within flower flies, the subfamily Eristalinae was recovered nonmonophyletic.
Display omitted
•Largest molecular dataset ever compiled to resolve relationships within Dytiscoidea.•The monophyly of the geographically disjunct Aspidytidae is hypothesized.•A clade of Amphizoidae ...and Aspidytidae is supported by most phylogenetic analyses.•Among-species compositional bias affects the inferred topologies within Dytiscoidea.
The beetle superfamily Dytiscoidea, placed within the suborder Adephaga, comprises six families. The phylogenetic relationships of these families, whose species are aquatic, remain highly contentious. In particular the monophyly of the geographically disjunct Aspidytidae (China and South Africa) remains unclear. Here we use a phylogenomic approach to demonstrate that Aspidytidae are indeed monophyletic, as we inferred this phylogenetic relationship from analyzing nucleotide sequence data filtered for compositional heterogeneity and from analyzing amino-acid sequence data. Our analyses suggest that Aspidytidae are the sister group of Amphizoidae, although the support for this relationship is not unequivocal. A sister group relationship of Hygrobiidae to a clade comprising Amphizoidae, Aspidytidae, and Dytiscidae is supported by analyses in which model assumptions are violated the least. In general, we find that both concatenation and the applied coalescent method are sensitive to the effect of among-species compositional heterogeneity. Four-cluster likelihood-mapping suggests that despite the substantial size of the dataset and the use of advanced analytical methods, statistical support is weak for the inferred phylogenetic placement of Hygrobiidae. These results indicate that other kinds of data (e.g. genomic meta-characters) are possibly required to resolve the above-specified persisting phylogenetic uncertainties. Our study illustrates various data-driven confounding effects in phylogenetic reconstructions and highlights the need for careful monitoring of model violations prior to phylogenomic analysis.
Adephaga is the second largest suborder of Coleoptera and contains aquatic and terrestrial groups that are sometimes classified as Hydradephaga and Geadephaga, respectively. The phylogenetic ...relationships of Adephaga have been studied intensively, but the relationships of the major subgroups of Geadephaga and the placement of Hygrobiidae within Dytiscoidea remain obscure. Here, we infer new DNA‐hybridization baits for exon‐capture phylogenomics and we combine new hybrid‐capture sequence data with transcriptomes to generate the largest phylogenomic taxon sampling within Adephaga presented to date. Our analyses show that the new baits are suitable to capture the target loci across different lineages of Adephaga. Phylogenetic analyses of moderately trimmed supermatrices confirm the hypothesis of paraphyletic ‘Hydradephaga’, with Gyrinidae placed as sister to all other families as in morphology‐based phylogenies, even though quartet‐concordance analyses did not support this result. All analyses conducted with site‐heterogeneous models suggest Trachypachidae as sister to a clade Carabidae + Cicindelidae in congruence with results from morphological studies. Haliplidae is inferred as sister to Dytiscoidea, while a clade of Noteridae (+ most likely Meruidae) is inferred as sister to all remaining Dytiscoidea. A strongly supported clade Hygrobiidae + (Amphizoidae + monophyletic Aspidytidae) is inferred in most analyses of moderately trimmed supermatrices when a site‐heterogeneous model is used. In general, we find that stringent trimming of supermatrices results in reduced deviation from model assumptions but also in reduction of phylogenetic information. We also find that site‐heterogeneous C60 models provide greater stability of phylogenetic relationships of Adephaga across analyses of different amino‐acid supermatrices than site‐homogeneous models. Thus, site‐heterogeneous C60 models can potentially reduce incongruence in phylogenomics. Lastly, we show that gene‐tree errors are prominent in the data, even after sub‐sampling genes to reduce these errors, but we also show that subsampling genes based on the likelihood mapping criterion in summary coalescent analyses results in higher topological congruence with the concatenation‐based tree. Overall, our analyses demonstrate that moderate alignment trimming strategies, application of site‐heterogeneous models and mitigation of gene‐tree errors should be routinely included in the phylogenomic pipeline in order to more accurately infer the phylogeny of species.
The most species‐rich phylogenomic analyses for the beetle suborder Adephaga are presented by combining new exon‐capture sequence data with transcriptomes.
Family‐level relationships of Adephaga are generally well resolved and largely congruent with morphology‐based phylogenies.
The use of empirical site‐heterogeneous mixture models results in greater stability of inferred phylogenetic relationships, whereas excessive trimming of supermatrices results in spurious phylogenetic estimates.
PDF
