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31 results for “phylotranscriptomics”
Amino acids (AA) all genes for: Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics
<p><b>Background:</b></p> <p>The largest radiation of animal life since the end Cretaceous extinction event 66 million years ago is that of schizophoran flies: a third of fly diversity including <i>Drosophila </i>lab fruit flies, house flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to understand the processes that contributed to the diversity of these agriculturally, medically, and forensically important flies. We use protein encoding sequence data from transcriptomes, including 3,145 genes from 70 species, representing all superfamilies, to improve the resolution of this previously intractable phylogenetic challenge.</p> <p><b>Results:</b></p> <p>Our results support a paraphyletic acalyptrate grade including a monophyletic Calyptratae and the monophyly of half of the acalyptrate superfamilies. The primary branching framework of Schizophora is well supported for the first time, revealing the primarily parasitic Pipunculidae and Sciomyzoidea s.l. as successive sister groups to the remaining Schizophora. Ephydroidea, <i>Drosophila</i>'s superfamily, is the sister group of Calyptratae. Sphaeroceroidea has modest support as the sister to all non-sciomyzoid Schizophora. We define two novel lineages corroborated by morphological traits, the Modified Oviscapt Clade containing Tephritoidea, Nerioidea, and other families, and the Cleft Pedicel Clade containg Calyptratae, Ephydroidea, and other families. Support values remain low among a challenging subset of lineages, including Diopsidae. The placement of these families remained uncertain in both concatenated maximum likelihood and multi-species coalescent approaches Rogue taxon removal was effective in increasing support values compared with strategies that maximize gene coverage or minimize missing data.</p> <p><b>Conclusions:</b></p> <p>Dividing most acalyptrate fly groups into four major lineages is supported consistently across analyses. Understanding the fundamental branching patterns of schizophoran flies provides a foundation for future comparative research on the genetics, ecology, and biocontrol.</p>
Data from: Phylotranscriptomics resolves ancient divergences in the Lepidoptera
Classic morphological studies of the oldest, so-called nonditrysian lineages of Lepidoptera yielded a well-resolved phylogeny, supported by the stepwise origin of the traits characterizing the clade Ditrysia, which contains over 98% of extant lepidopterans. Subsequent polymerase chain reaction (PCR)-based molecular studies have robustly supported many aspects of the morphological hypothesis and strongly contradicted others, while leaving some relationships unsettled. Here we bring the greatly expanded gene sampling of RNA-Seq to bear on nonditrysian phylogeny, especially those aspects that were not conclusively resolved by the combination of morphology and previous PCR-based multi-gene studies. We analysed up to 2212 genes in each of 28 species representing all 12 superfamilies and 15 of 21 families of nonditrysians, plus trichopteran outgroups and representative Ditrysia. Our maximum likelihood phylogeny estimates used both nonsynonymous changes only (degen1 coding) and all nucleotides (nt123) partitioned by codon position, recovering a novel hypothesis for early glossatan relationships that is the most strongly supported to date. We find strong support for Micropterigidae alone as the sister group to all other Lepidoptera, in agreement with morphology and early molecular evidence, but in contrast to recent PCR-based studies. Also very strongly supported are the previously recognized clades Angiospermivora, Heteroneura, Eulepidoptera and Euheteroneura. Finally, we find strong support for paraphyly of the southern hemisphere family Palaephatidae, with the South American genus Palaephatus Butler forming the previously undetermined sister group to Ditrysia. The remaining palaephatids, Australian and South American, form the sister group to Tischeriidae.
Assemblies and alignments from a study on the phylotranscriptomic relationships of Oophila, a genus of green algae associated to amphibian egg masses
<p>Dataset for:</p> <p>Vences M, Sachs M, Irisarri I, Bartels F, Eriksson PF, Künzel S, Kurabayashi A, Laugen AT, Vegso ZT, Bishop CD, Kerney R, Arndt H. Phylotranscriptomic relationships of the Oophila clade of green algae associated to amphibian egg masses. Mol Phylogenet Evol. 2024 Aug 6:108165. doi: 10.1016/j.ympev.2024.108165. </p>
Data from: Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny
An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. Yet many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often under-sampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing Expressed Sequence Tag (EST), mitochondrial genome, nuclear genome and rDNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, Pentastomida); Multicrustacea (Copepoda, Malacostraca, Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Brachiopoda+Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. Yet, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a 'total evidence' philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylogenetic insights into long-standing questions, especially when carefully analyzed in combination with other data.
Datasets used for Western Mediterranean Dugesia phylotranscriptomic analyses
<p><span>The Mediterranean is one of the most biodiverse areas of the Paleartic region. Here, basing on large data sets of single copy orthologs obtained from transcriptomic data, we investigated the evolutionary history of the genus <em>Dugesia</em> in the Western Mediterranean area. The results corroborated that the complex paleogeological history of the region was an important driver of diversification for the genus, speciating as microplates and islands were forming. These processes led to the differentiation of three main biogeographic clades: Iberia-Apennines-Alps, Corsica-Sardinia, and Iberia-Africa. The internal relationships of these major clades were analysed with several representative samples per species. The use of large data sets regarding the number of <em>loci</em> and samples, as well as state-of-the-art phylogenomic inference methods allowed us to answer different unresolved questions about the evolution of particular groups, such as the diversification path of <em>D. subtentaculata</em> in the Iberian Peninsula and its colonization of Africa. Additionally, our results support the differentiation of <em>D. benazzii</em> in two lineages which could represent two species. Finally, we analysed here for the first time a comprehensive number of samples from several asexual Iberian populations whose assignment at the species level has been an enigma through the years. The phylogenies obtained with different inference methods showed a branching topology of asexual individuals at the base of sexual clades. We hypothesize that this unexpected topology is related to long-term asexuality. This work represents the first phylotranscriptomic analysis of Tricladida, laying the first stone of the genomic era in phylogenetic studies on this taxonomic group.</span></p>
Phylotranscriptomics reveal the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution
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Datasets used for Western Mediterranean Dugesia phylotranscriptomic analyses
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Data from: Phylotranscriptomics resolves ancient divergences in the Lepidoptera
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Amino acids (AA) all genes for: Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics
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Data from: Arthropod phylotranscriptomics with a special focus on the basal phylogeny of the Myriapoda
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Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints
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Data from: Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny
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Data from: Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae)
A robust phylogeny is prerequisite to understand the evolution and biogeography of organisms. However, ancient and recent evolutionary radiations occurred in many plant lineages, which pose great challenges for phylogenetic analysis, especially for conifers characterized by large effective population sizes and long generation times. Picea is an important component of the dark coniferous forests in the Northern Hemisphere. Previous studies improved our understanding of its evolutionary history, but its interspecific relationships and biogeographic history remain largely unresolved. In the present study, we reconstructed a well-resolved phylogeny of Picea by comparative transcriptomic analysis based on a complete species sampling. The phylogenetic analysis, together with molecular dating and ancestral area reconstruction, further supports the North American origin hypothesis for Picea, and indicates that this genus experienced multiple out-of-North America dispersals by the Bering Land Bridge. We also found that spruces in the Japanese Archipelago have multiple origins, and P. morrisonicola from the Taiwan Island has a close relationship with species from the Qinghai-Tibetan Plateau and adjacent regions. Our study provides the first complete phylogeny of Picea at the genomic level, which is important for future studies of this genus.
Data from: Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)
Premise of Study: The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated ten transcriptomes and incorporated existing RNA-seq data to infer a multi-locus nuclear phylogeny of the Cypripedioideae and to determine if a whole genome duplication event (WGD) correlated to the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families. Methods: Transcriptome data was used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree. Key results: Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny. Conclusions: Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.
Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia)
<p>BLASTn summary</p> <p>Phylogenetic data matrices and trees</p>
Fig. 1 in Mimopidae is the sister group to all other scolopendromorph centipedes (Chilopoda, Scolopendromorpha): a phylotranscriptomic approach
Fig. 1 Life habitus of Mimops orientalis Kraepelin, 1903, from Dongshan Forest Park, Zhashui county, Shangluo, Shaanxi province, China
Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae
<p class="western">The volvocine algae, which include the single-celled species <i>Chlamydomonas reinhardtii</i> and the colonial species <i>Volvox carteri</i>, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the history of this group have by and large relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. As a result, volvocine phylogenies lack concordance depending on the number and/or type of genes (i.e., chloroplast vs nuclear) chosen for phylogenetic inference. While multiple studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group, other studies call into question one or more of these conclusions. An accurate assessment of the evolutionary history of the volvocine algae requires inference of a more robust phylogeny. We performed RNA sequencing (RNA-seq) on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We then compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes, and subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation arose independently at least four, and possibly as many as six times, within the volvocine algae. Altogether, our results demonstrate that multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming the importance of this group as a model system for the study of major transitions in the history of life.</p>
Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales
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Data from: Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae)
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Data from: Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)
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