scholarly journals Using ultraconserved elements to reconstruct the termite tree of life

2021 ◽  
Author(s):  
Simon Hellemans ◽  
Menglin Wang ◽  
Nonno Hasegawa ◽  
Jan Šobotník ◽  
Rudolf H. Scheffrahn ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Taxonomic Revision ◽  
Mitochondrial Genomes ◽  
Species Trees ◽  
Ultraconserved Elements ◽  
Three Samples ◽  
Museum Samples ◽  
History Of ◽  
Genome Assemblies ◽  
Low Coverage

AbstractThe phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting 50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of Cryptocercus, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted in silico between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: https://github.com/oist/TER-UCE-DB/.

scholarly journals A molecular phylogeny of the genus Echinococcus inferred from complete mitochondrial genomes

Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 713-722 ◽  
Author(s):  
M. NAKAO ◽  
D. P. McMANUS ◽  
P. M. SCHANTZ ◽  
P. S. CRAIG ◽  
A. ITO
Keyword(s):  
North America ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Taxonomic Revision ◽  
Sensu Stricto ◽  
Amino Acid Sequences ◽  
Mitochondrial Genomes ◽  
Land Bridge ◽  
High Level ◽  
Complete Mitochondrial Genomes

SUMMARYTaxonomic revision by molecular phylogeny is needed to categorize members of the genus Echinococcus (Cestoda: Taeniidae). We have reconstructed the phylogenetic relationships of E. oligarthrus, E. vogeli, E. multilocularis, E. shiquicus, E. equinus, E. ortleppi, E. granulosus sensu stricto and 3 genotypes of E. granulosus sensu lato (G6, G7 and G8) from their complete mitochondrial genomes. Maximum likelihood and partitioned Bayesian analyses using concatenated data sets of nucleotide and amino acid sequences depicted phylogenetic trees with the same topology. The 3 E. granulosus genotypes corresponding to the camel, pig, and cervid strains were monophyletic, and their high level of genetic similarity supported taxonomic species unification of these genotypes into E. canadensis. Sister species relationships were confirmed between E. ortleppi and E. canadensis, and between E. multilocularis and E. shiquicus, regardless of the analytical approach employed. The basal positions of the phylogenetic tree were occupied by the neotropical endemic species, E. oligarthrus and E. vogeli, whose definitive hosts are derived from carnivores that immigrated from North America after the formation of the Panamanian land bridge. Host-parasite co-evolution comparisons suggest that the ancestral homeland of Echinococcus was North America or Asia, depending on whether the ancestral definitive hosts were canids or felids.

scholarly journals A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies

2019 ◽  
Vol 5 ◽  
Author(s):  
Alexis Criscuolo
Keyword(s):  
Phylogenetic Trees ◽  
Species Trees ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Internal Branch ◽  
Multiple Sequence Alignments ◽  
Fast Running ◽  
Alignment Free ◽  
Multiple Threads ◽  
Genome Assemblies

This paper describes a novel alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences using publicly available bioinformatics tools. For each pair of genomes, a dissimilarity measure is first computed and next transformed to obtain an estimation of the number of substitution events that have occurred during their evolution. These pairwise evolutionary distances are then used to infer a phylogenetic tree and assess a confidence support for each internal branch. Analyses of both simulated and real genome datasets show that this bioinformatics procedure allows accurate phylogenetic trees to be reconstructed with fast running times, especially when launched on multiple threads. Implemented in a publicly available script, named JolyTree, this procedure is a useful approach for quickly inferring species trees without the burden and potential biases of multiple sequence alignments.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals Mice as stowaways? Colonization history of Danish striped field mice

2017 ◽  
Vol 13 (7) ◽  
pp. 20170064 ◽  
Author(s):  
Liselotte Wesley Andersen ◽  
Magnus Jacobsen ◽  
Christina Vedel-Smith ◽  
Thomas Secher Jensen
Keyword(s):  
Eastern Europe ◽  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Field Mouse ◽  
Colonization History ◽  
Striped Field Mouse ◽  
Steppe Region ◽  
History Of ◽  
Field Mice ◽  
Human Introduction

Species from the steppe region of Eastern Europe likely colonized northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse ( Apodemus agrarius Pallas, 1783), is a steppe-derived species often found in human crops. It is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe since approximately 10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland.

scholarly journals Exploring and Reconstructing Ancestral Anatomies using Ontology-Informed Approaches

2019 ◽  
Vol 3 ◽  
Author(s):  
Sergei Tarasov ◽  
Istvan Miko ◽  
Matthew Yoder ◽  
Josef Uyeda
Keyword(s):  
Phylogenetic Trees ◽  
Character State ◽  
Ancestral Reconstruction ◽  
Anatomy Ontology ◽  
Insect Order ◽  
Ancestral Character State ◽  
Body Regions ◽  
Individual Traits ◽  
History Of ◽  
Complex Characters

Ancestral character state reconstruction has been long used to gain insight into the evolution of individual traits in organisms. However, organismal anatomies (= entire phenotypes) are not merely ensembles of individual traits, rather they are complex systems where traits interact with each other due to anatomical dependencies (when one trait depends on the presence of another trait) and developmental constraints. Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of entire organismal anatomies or organismal body regions. Herein, we present a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies, Tarasov and Uyeda 2019) that takes into account anatomical dependencies and uses stochastic maps (i.e., phylogenetic trees with an instance of mapped evolutionary history of characters, Huelsenbeck et al. 2003) along with anatomy ontologies to reconstruct organismal anatomies. Our approach treats the entire phenotype or its component body regions as single complex characters and allows exploring and comparing phenotypic evolution at different levels of anatomical hierarchy. These complex characters are constructed by ontology-informed amalgamation of elementary characters (i.e., those coded in character matrix) using stochastic maps. In our approach, characters are linked with the terms from an anatomy ontology, which allows viewing them not just as an ensemble of character state tokens but as entities that have their own biological meaning provided by the ontology. This ontology-informed framework provides new opportunities for tracking phenotypic radiations and anatomical evolution of organisms, which we explore using a large dataset for the insect order Hymenoptera (sawflies, wasps, ants and bees).

scholarly journals Discordant evolution of organellar genomes in peas (Pisum L.)

2020 ◽  
Author(s):  
Vera S. Bogdanova ◽  
Natalia V. Shatskaya ◽  
Anatoliy V. Mglinets ◽  
Oleg E. Kosterin ◽  
Gennadiy V. Vasiliev
Keyword(s):  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Plant Evolution ◽  
Hybrid Origin ◽  
Mitochondrial Genomes ◽  
North East ◽  
Plastid Genomes ◽  
First Time ◽  
Evolutionary Fate

AbstractPlastids and mitochondria have their own small genomes which do not undergo meiotic recombination and may have evolutionary fate different from each other and nuclear genome, thus highlighting interesting phenomena in plant evolution. We for the first time sequenced mitochondrial genomes of pea (Pisum L.), in 38 accessions mostly representing diverse wild germplasm from all over pea geographical range. Six structural types of pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Bayesian phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant implying not less than six events of hybridisation of diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles is supposed to have been driven by plastid-nuclear incompatibility, known to be widespread in pea wide crosses and apparently shaping the organellar phylogenies. The topology of a phylogenetic tree based on the nucleotide sequence of a nuclear gene His5 coding for a histone H1 subtype corresponds to the current taxonomy and resembles that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin resulting from crosses of peas similar to those presently inhabiting south-east and north-east Mediterranean in broad sense.

scholarly journals The pink salmon genome: uncovering the genomic consequences of a strict two-year life-cycle

2021 ◽  
Author(s):  
Kris A. Christensen ◽  
Eric B. Rondeau ◽  
Dionne Sakhrani ◽  
Carlo A. Biagi ◽  
Hollie Johnson ◽  
...  
Keyword(s):  
Pacific Salmon ◽  
Pink Salmon ◽  
Chromosomal Polymorphism ◽  
Oncorhynchus Gorbuscha ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Temporal Isolation ◽  
History Of ◽  
Genome Assemblies ◽  
Salmon Fishery

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A strict two-year life-history of most pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

scholarly journals UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

2021 ◽  
Vol 9 ◽  
Author(s):  
Caio Ribeiro ◽  
Lucas Oliveira ◽  
Romina Batista ◽  
Marcos De Sousa
Keyword(s):  
Best Practices ◽  
Software Package ◽  
Phylogenetic Trees ◽  
Computational Analysis ◽  
Data Matrix ◽  
Command Line ◽  
Command Line Interface ◽  
Ultraconserved Elements ◽  
Research Software ◽  
Different Levels

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

scholarly journals The Evolutionary History of the Chymase Locus -a Locus Encoding Several of the Major Hematopoietic Serine Proteases

2021 ◽  
Vol 22 (20) ◽  
pp. 10975
Author(s):  
Srinivas Akula ◽  
Zhirong Fu ◽  
Sara Wernersson ◽  
Lars Hellman
Keyword(s):  
Mast Cell ◽  
T Cell ◽  
Serine Proteases ◽  
Phylogenetic Trees ◽  
Granzyme B ◽  
Large Family ◽  
Cathepsin G ◽  
Immune Functions ◽  
New Class ◽  
History Of

Several hematopoietic cells of the immune system store large amounts of proteases in cytoplasmic granules. The absolute majority of these proteases belong to the large family of chymotrypsin-related serine proteases. The chymase locus is one of four loci encoding these granule-associated serine proteases in mammals. The chymase locus encodes only four genes in primates, (1) the gene for a mast-cell-specific chymotryptic enzyme, the chymase; (2) a T-cell-expressed asp-ase, granzyme B; (3) a neutrophil-expressed chymotryptic enzyme, cathepsin G; and (4) a T-cell-expressed chymotryptic enzyme named granzyme H. Interestingly, this locus has experienced a number of quite dramatic expansions during mammalian evolution. This is illustrated by the very large number of functional protease genes found in the chymase locus of mice (15 genes) and rats (18 genes). A separate expansion has also occurred in ruminants, where we find a new class of protease genes, the duodenases, which are expressed in the intestinal region. In contrast, the opossum has only two functional genes in this locus, the mast cell (MC) chymase and granzyme B. This low number of genes may be the result of an inversion, which may have hindered unequal crossing over, a mechanism which may have been a major factor in the expansion within the rodent lineage. The chymase locus can be traced back to early tetrapods as genes that cluster with the mammalian genes in phylogenetic trees can be found in frogs, alligators and turtles, but appear to have been lost in birds. We here present the collected data concerning the evolution of this rapidly evolving locus, and how these changes in gene numbers and specificities may have affected the immune functions in the various tetrapod species.

scholarly journals treeWidget: a BioJS component to visualise phylogenetic trees

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 49 ◽  
Author(s):  
Fabian Schreiber
Keyword(s):  
Phylogenetic Trees ◽  
Protein Domains ◽  
Gene Families ◽  
Sequence Information ◽  
Gene Duplications ◽  
Link Type ◽  
History Of ◽  
Conservation Patterns ◽  
Evolution Of Gene Families ◽  
The Web

Summary: Phylogenetic trees are widely used to represent the evolution of gene families. As the history of gene families can be complex (including lots of gene duplications), its visualisation can become a difficult task. A good/accurate visualisation of phylogenetic trees - especially on the web - allows easier understanding and interpretation of trees to help to reveal the mechanisms that shape the evolution of a specific set of gene/species. Here, I present treeWidget, a modular BioJS component to visualise phylogenetic trees on the web. Through its modularity, treeWidget can be easily customized to allow the display of sequence information, e.g. protein domains and alignment conservation patterns.Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7707

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