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Mobile Elements in Phylogenomic Reconstructions

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (22 March 2022) | Viewed by 51353

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Prof. Dr. Jürgen Schmitz

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Guest Editor

Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
Interests: jumping genes as phylogenetic markers; incomplete lineage sorting; homoplasy; methods in applied retrophylogenomics

Dr. Liliya Doronina

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Guest Editor

Special Issue Information

Dear Colleagues,

It is our great pleasure to invite your contributions to a Special Issue of Genes: “Mobile Elements in Phylogenomic Reconstructions”.

Retrotransposed elements (REs), a special class of transposable units that arise via reverse transcription of RNA intermediates and subsequent insertion, comprise a substantial proportion of eukaryotic genomes (e.g., ~45% of human, ~10% of zebra finch, ~55% of zebrafish, ~20% of drosophila, ~80% of maize). Their insertion, while not continuous over time, is largely random and virtually homoplasy-free. Their presence/absence patterns provide historical evidence of speciation events, making them excellent phylogenomic markers. Elements shared at orthologous positions in the genomes of two related species and their clear absence in other lineages are evidence of their phylogenetic affiliation. Depending on the ancestral timeframe of speciation events of a given lineage, incomplete lineage sorting may somewhat confound these patterns, necessitating special multidirectional screening strategies to clarify evolutionary reconstructions. Today, however, many such computational tools exist and are available to evolutionary scientists everywhere to partially automate these screenings. REs have now been used to significantly resolve the conundrums present in many phylogenetic trees. This Special Issue will be unique in presenting methodologies and strategies of exploring phylogenetically diagnostic REs and their usefulness in revealing new phylogenies.

Prof. Dr. Jürgen Schmitz
Dr. Liliya Doronina
Guest Editors

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Keywords

mobile elements
transposable elements
retrotransposons
retrophylogenomics
presence/absence markers
incomplete lineage sorting
random insertion sites
homoplasy-free

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Published Papers (10 papers)

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30 pages, 5090 KiB

Open AccessArticle

Phylogenomic Coalescent Analyses of Avian Retroelements Infer Zero-Length Branches at the Base of Neoaves, Emergent Support for Controversial Clades, and Ancient Introgressive Hybridization in Afroaves

by John Gatesy and Mark S. Springer

Genes 2022, 13(7), 1167; https://doi.org/10.3390/genes13071167 - 28 Jun 2022

Cited by 1 | Viewed by 3408

Abstract

Retroelement insertions (RIs) are low-homoplasy characters that are ideal data for addressing deep evolutionary radiations, where gene tree reconstruction errors can severely hinder phylogenetic inference with DNA and protein sequence data. Phylogenomic studies of Neoaves, a large clade of birds (>9000 species) that first diversified near the Cretaceous–Paleogene boundary, have yielded an array of robustly supported, contradictory relationships among deep lineages. Here, we reanalyzed a large RI matrix for birds using recently proposed quartet-based coalescent methods that enable inference of large species trees including branch lengths in coalescent units, clade-support, statistical tests for gene flow, and combined analysis with DNA-sequence-based gene trees. Genome-scale coalescent analyses revealed extremely short branches at the base of Neoaves, meager branch support, and limited congruence with previous work at the most challenging nodes. Despite widespread topological conflicts with DNA-sequence-based trees, combined analyses of RIs with thousands of gene trees show emergent support for multiple higher-level clades (Columbea, Passerea, Columbimorphae, Otidimorphae, Phaethoquornithes). RIs express asymmetrical support for deep relationships within the subclade Afroaves that hints at ancient gene flow involving the owl lineage (Strigiformes). Because DNA-sequence data are challenged by gene tree-reconstruction error, analysis of RIs represents one approach for improving gene tree-based methods when divergences are deep, internodes are short, terminal branches are long, and introgressive hybridization further confounds species–tree inference. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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15 pages, 2921 KiB

Open AccessArticle

paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences

by Raphael Steffen, Lynn Ogoniak, Norbert Grundmann, Anna Pawluchin, Oliver Soehnlein and Jürgen Schmitz

Genes 2022, 13(6), 1090; https://doi.org/10.3390/genes13061090 - 18 Jun 2022

Cited by 5 | Viewed by 5442

Abstract

Evolution is change over time. Although neutral changes promoted by drift effects are most reliable for phylogenetic reconstructions, selection-relevant changes are of only limited use to reconstruct phylogenies. On the other hand, comparative analyses of neutral and selected changes of protein-coding DNA sequences (CDS) retrospectively tell us about episodic constrained, relaxed, and adaptive incidences. The ratio of sites with nonsynonymous (amino acid altering) versus synonymous (not altering) mutations directly measures selection pressure and can be analysed by using the Phylogenetic Analysis by Maximum Likelihood (PAML) software package. We developed a CDS extractor for compiling protein-coding sequences (CDS-extractor) and parallel PAML (paPAML) to simplify, amplify, and accelerate selection analyses via parallel processing, including detection of negatively selected sites. paPAML compiles results of site, branch-site, and branch models and detects site-specific negative selection with the output of a codon list labelling significance values. The tool simplifies selection analyses for casual and inexperienced users and accelerates computing speeds up to the number of allocated computer threads. We then applied paPAML to examine the evolutionary impact on a new GINS Complex Subunit 3 exon, and neutrophil-associated as well as lysin and apolipoprotein genes. Compared with codeml (PAML version 4.9j) and HyPhy (HyPhy FEL version 2.5.26), all paPAML test runs performed with 10 computing threads led to identical selection pressure results, whereas the total selection analysis via paPAML, including all model comparisons, was about 3 to 5 times faster than the longest running codeml model and about 7 to 15 times faster than the entire processing time of these codeml runs. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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14 pages, 1618 KiB

Open AccessArticle

Mobilome of Apicomplexa Parasites

by Matias Rodriguez and Wojciech Makalowski

Genes 2022, 13(5), 887; https://doi.org/10.3390/genes13050887 - 16 May 2022

Cited by 3 | Viewed by 3505

Abstract

Transposable elements (TEs) are mobile genetic elements found in the majority of eukaryotic genomes. Genomic studies of protozoan parasites from the phylum Apicomplexa have only reported a handful of TEs in some species and a complete absence in others. Here, we studied sixty-four Apicomplexa genomes available in public databases, using a ‘de novo’ approach to build candidate TE models and multiple strategies from known TE sequence databases, pattern recognition of TEs, and protein domain databases, to identify possible TEs. We offer an insight into the distribution and the type of TEs that are present in these genomes, aiming to shed some light on the process of gains and losses of TEs in this phylum. We found that TEs comprise a very small portion in these genomes compared to other organisms, and in many cases, there are no apparent traces of TEs. We were able to build and classify 151 models from the TE consensus sequences obtained with RepeatModeler, 96 LTR TEs with LTRpred, and 44 LINE TEs with MGEScan. We found LTR Gypsy-like TEs in Eimeria, Gregarines, Haemoproteus, and Plasmodium genera. Additionally, we described LINE-like TEs in some species from the genera Babesia and Theileria. Finally, we confirmed the absence of TEs in the genus Cryptosporidium. Interestingly, Apicomplexa seem to be devoid of Class II transposons. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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9 pages, 1732 KiB

Open AccessArticle

Euarchontoglires Challenged by Incomplete Lineage Sorting

by Liliya Doronina, Olga Reising, Hiram Clawson, Gennady Churakov and Jürgen Schmitz

Genes 2022, 13(5), 774; https://doi.org/10.3390/genes13050774 - 27 Apr 2022

Cited by 3 | Viewed by 5413

Abstract

Euarchontoglires, once described as Supraprimates, comprise primates, colugos, tree shrews, rodents, and lagomorphs in a clade that evolved about 90 million years ago (mya) from a shared ancestor with Laurasiatheria. The rapid speciation of groups within Euarchontoglires, and the subsequent inherent incomplete marker fixation in ancestral lineages, led to challenged attempts at phylogenetic reconstructions, particularly for the phylogenetic position of tree shrews. To resolve this conundrum, we sampled genome-wide presence/absence patterns of transposed elements (TEs) from all representatives of Euarchontoglires. This specific marker system has the advantage that phylogenetic diagnostic characters can be extracted in a nearly unbiased fashion genome-wide from reference genomes. Their insertions are virtually free of homoplasy. We simultaneously employed two computational tools, the genome presence/absence compiler (GPAC) and 2-n-way, to find a maximum of diagnostic insertions from more than 3 million TE positions. From 361 extracted diagnostic TEs, 132 provide significant support for the current resolution of Primatomorpha (Primates plus Dermoptera), 94 support the union of Euarchonta (Primates, Dermoptera, plus Scandentia), and 135 marker insertion patterns support a variety of alternative phylogenetic scenarios. Thus, whole genome-level analysis and a virtually homoplasy-free marker system offer an opportunity to finally resolve the notorious phylogenetic challenges that nature produces in rapidly diversifying groups. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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17 pages, 1952 KiB

Open AccessArticle

Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone

by Liliya Doronina, Graham M. Hughes, Diana Moreno-Santillan, Colleen Lawless, Tadhg Lonergan, Louise Ryan, David Jebb, Bogdan M. Kirilenko, Jennifer M. Korstian, Liliana M. Dávalos, Sonja C. Vernes, Eugene W. Myers, Emma C. Teeling, Michael Hiller, Lars S. Jermiin, Jürgen Schmitz, Mark S. Springer and David A. Ray

Genes 2022, 13(5), 766; https://doi.org/10.3390/genes13050766 - 26 Apr 2022

Cited by 10 | Viewed by 5321

Abstract

Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest divergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto unsampled laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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13 pages, 1435 KiB

Open AccessArticle

Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics

by Jessica M. Storer, Jerilyn A. Walker, Catherine E. Rockwell, Grayce Mores, Thomas O. Beckstrom, Joseph D. Orkin, Amanda D. Melin, Kimberley A. Phillips, Christian Roos and Mark A. Batzer

Genes 2022, 13(4), 572; https://doi.org/10.3390/genes13040572 - 24 Mar 2022

Cited by 4 | Viewed by 4057

Abstract

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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13 pages, 2794 KiB

Open AccessArticle

SINE-Based Phylogenomics Reveal Extensive Introgression and Incomplete Lineage Sorting in Myotis

by Jennifer M. Korstian, Nicole S. Paulat, Roy N. Platt II, Richard D. Stevens and David A. Ray

Genes 2022, 13(3), 399; https://doi.org/10.3390/genes13030399 - 23 Feb 2022

Cited by 14 | Viewed by 3466

Abstract

Using presence/absence data from over 10,000 Ves SINE insertions, we reconstructed a phylogeny for 11 Myotis species. With nearly one-third of individual Ves gene trees discordant with the overall species tree, phylogenetic conflict appears to be rampant in this genus. From the observed conflict, we infer that ILS is likely a major contributor to the discordance. Much of the discordance can be attributed to the hypothesized split between the Old World and New World Myotis clades and with the first radiation of Myotis within the New World. Quartet asymmetry tests reveal signs of introgression between Old and New World taxa that may have persisted until approximately 8 MYA. Our introgression tests also revealed evidence of both historic and more recent, perhaps even contemporary, gene flow among Myotis species of the New World. Our findings suggest that hybridization likely played an important role in the evolutionary history of Myotis and may still be happening in areas of sympatry. Despite limitations arising from extreme discordance, our SINE-based phylogeny better resolved deeper relationships (particularly the positioning of M. brandtii) and was able to identify potential introgression pathways among the Myotis species sampled. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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20 pages, 4763 KiB

Open AccessFeature PaperArticle

Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes

by James D. Galbraith, Alastair J. Ludington, Kate L. Sanders, Timothy G. Amos, Vicki A. Thomson, Daniel Enosi Tuipulotu, Nathan Dunstan, Richard J. Edwards, Alexander Suh and David L. Adelson

Genes 2022, 13(2), 217; https://doi.org/10.3390/genes13020217 - 25 Jan 2022

Cited by 3 | Viewed by 7453

Abstract

Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo–Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~30 Mya and have since rapidly diversified into six amphibious, ~60 marine and ~100 terrestrial species that fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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Review

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16 pages, 2850 KiB

Open AccessReview

SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics

by Masato Nikaido, Hidenori Nishihara and Norihiro Okada

Genes 2022, 13(6), 989; https://doi.org/10.3390/genes13060989 - 31 May 2022

Cited by 7 | Viewed by 5684

Abstract

Currently, the insertions of SINEs (and other retrotransposed elements) are regarded as one of the most reliable synapomorphies in molecular systematics. The methodological mainstream of molecular systematics is the calculation of nucleotide (or amino acid) sequence divergences under a suitable substitution model. In contrast, SINE insertion analysis does not require any complex model because SINE insertions are unidirectional and irreversible. This straightforward methodology was named the “SINE method,” which resolved various taxonomic issues that could not be settled by sequence comparison alone. The SINE method has challenged several traditional hypotheses proposed based on the fossil record and anatomy, prompting constructive discussions in the Evo/Devo era. Here, we review our pioneering SINE studies on salmon, cichlids, cetaceans, Afrotherian mammals, and birds. We emphasize the power of the SINE method in detecting incomplete lineage sorting by tracing the genealogy of specific genomic loci with minimal noise. Finally, in the context of the whole-genome era, we discuss how the SINE method can be applied to further our understanding of the tree of life. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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23 pages, 2563 KiB

Open AccessFeature PaperReview

Methodologies for the De novo Discovery of Transposable Element Families

by Jessica M. Storer, Robert Hubley, Jeb Rosen and Arian F. A. Smit

Genes 2022, 13(4), 709; https://doi.org/10.3390/genes13040709 - 17 Apr 2022

Cited by 14 | Viewed by 6030

Abstract

The discovery and characterization of transposable element (TE) families are crucial tasks in the process of genome annotation. Careful curation of TE libraries for each organism is necessary as each has been exposed to a unique and often complex set of TE families. De novo methods have been developed; however, a fully automated and accurate approach to the development of complete libraries remains elusive. In this review, we cover established methods and recent developments in de novo TE analysis. We also present various methodologies used to assess these tools and discuss opportunities for further advancement of the field. Full article

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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