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Untangling Host-Symbiont Coevolutionary History in the High Throughput Sequencing (HTS)...
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Untangling Host-Symbiont Coevolutionary History in the High Throughput Sequencing (HTS) Era

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Evolutionary Biology".

Deadline for manuscript submissions: 29 November 2024 | Viewed by 6028

Special Issue Editors

Dr. Jorge Doña

E-Mail Website
Guest Editor
1. Illinois Natural History Survey, Champaign, IL 61820, USA
2. Departamento de Biología Animal, University of Granada, 18001 Granada, Spain
Interests: molecular ecology; host-symbiont interactions; speciation; hybridization; feather mites; feather lice; population genetics; cophylogenetics; macroecology; DNA Barcoding; DNA metabarcoding; microbiomes; molecular taxonomy; species delimitation; high-throughput sequencing; bioinformatics
Dr. Andrew D. Sweet

E-Mail Website
Guest Editor
Department of Biological Sciences, Arkansas State University, State University, AR 72467, USA

Special Issue Information

Dear Colleagues,

High-throughput sequencing (HTS) and “-omics” datasets play an increasingly prominent role in most subfields of ecology and evolution. One of the areas profoundly impacted by these high-throughput sequencing approaches is the study of host–symbiont coevolution (“coevolution” used here in a broader sense encompassing any comparison of hosts and their symbionts in an evolutionary framework). In recent years, there has been a particular increase in the use of “-omics” datasets to understand how hosts and their symbionts interact over evolutionary time. This work has certainly progressed the field of host–symbiont coevolution, but there remain many avenues yet to be investigated. For example, genomic introgression, which can be easily detected in multi-gene datasets, may impact cophylogenetic reconstructions, but it is poorly studied in host–symbiont systems.

In this Special Issue, we seek to bring together empirical, methodological, or theoretical papers that will advance our overall knowledge of host–symbiont coevolutionary history, especially on cutting-edge topics that utilize HTS data. HTS data include, but are not limited to, genomes/transcriptomes/epigenomes, multi-gene datasets, SNPs, or symbiont-associated microbial metagenomes. Examples of preferential topics include cophylogenetic methods, epigenetics, gene expression, genome architecture, genome evolution, hybridization, microbiomes, phylogenomics, phylogeography, phylosymbiosis, population genomics, and transcriptomics.

The scope is very broad, and we encourage any submissions that are useful to the field of host–symbiont coevolution, including preliminary results or small-scale studies. Additionally, there is an updated deadline for submissions (December 2021). Please do not hesitate to inquire about whether an idea may fit in the Special Issue.

Dr. Jorge Doña
Dr. Andrew D. Sweet
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cophylogenetic methods
  • ectosymbionts
  • endosymbionts
  • epigenetics
  • introgression
  • long-read sequencing
  • genome architecture
  • genome evolution
  • hybridization
  • microbiomes
  • mutualist
  • parasite
  • phylogenomics
  • phylogeography
  • phylosymbiosis
  • population genomics
  • transcriptomics

Published Papers (3 papers)

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Research

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19 pages, 1583 KiB  
Article
Population Genomics of Pooled Samples: Unveiling Symbiont Infrapopulation Diversity and Host–Symbiont Coevolution
by Alix E. Matthews, Than J. Boves, Katie L. Percy, Wendy M. Schelsky and Asela J. Wijeratne
Life 2023, 13(10), 2054; https://doi.org/10.3390/life13102054 - 14 Oct 2023
Viewed by 956
Abstract
Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host–symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome [...] Read more.
Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host–symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome those barriers is to pool multiple individuals from the same infrapopulation (i.e., individual host) and sequence them together (Pool-Seq), but individual-level information is then compromised. To simultaneously address both issues (i.e., minimal DNA yields and loss of individual-level information), we implemented a strategic Pool-Seq approach to assess variation in sequencing performance and categorize genetic diversity (single nucleotide polymorphisms (SNPs)) at both the individual-level and infrapopulation-level for microscopic feather mites. To do so, we collected feathers harboring mites (Proctophyllodidae: Amerodectes protonotaria) from four individual Prothonotary Warblers (Parulidae: Protonotaria citrea). From each of the four hosts (i.e., four mite infrapopulations), we conducted whole-genome sequencing on three extraction pools consisting of different numbers of mites (1 mite, 5 mites, and 20 mites). We found that samples containing pools of multiple mites had more sequencing reads map to the feather mite reference genome than did the samples containing only a single mite. Mite infrapopulations were primarily genetically structured by their associated individual hosts (not pool size) and the majority of SNPs were shared by all pools within an infrapopulation. Together, these results suggest that the patterns observed are driven by evolutionary processes occurring at the infrapopulation level and are not technical signals due to pool size. In total, despite the challenges presented by microscopic symbionts in HTS studies, this work highlights the value of both individual-level and infrapopulation-level sequencing toward our understanding of host–symbiont coevolution at multiple evolutionary scales. Full article
(This article belongs to the Special Issue Untangling Host-Symbiont Coevolutionary History in the High Throughput Sequencing (HTS) Era)
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14 pages, 616 KiB  
Article
Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses
by Ran Libeskind-Hadas
Life 2022, 12(3), 443; https://doi.org/10.3390/life12030443 - 17 Mar 2022
Cited by 4 | Viewed by 2199
Abstract
Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. This paper provides an overview of the underlying theory of reconciliation in the context of host-symbiont cophylogenetics, identifying some of the major challenges to users of these methods, such [...] Read more.
Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. This paper provides an overview of the underlying theory of reconciliation in the context of host-symbiont cophylogenetics, identifying some of the major challenges to users of these methods, such as selecting event costs and selecting representative reconciliations. Next, recent advances to address these challenges are discussed followed by a discussion of several established and recent software tools. Full article
(This article belongs to the Special Issue Untangling Host-Symbiont Coevolutionary History in the High Throughput Sequencing (HTS) Era)
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Review

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17 pages, 511 KiB  
Review
Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice
by Kevin P. Johnson
Life 2022, 12(9), 1442; https://doi.org/10.3390/life12091442 - 16 Sep 2022
Cited by 1 | Viewed by 1711
Abstract
Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated [...] Read more.
Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated to date, and these have opened up new resources for the study of louse biology. Whole genome sequencing has been used to assemble large phylogenomic datasets for lice, incorporating sequences of thousands of genes. These datasets have provided highly supported trees at all taxonomic levels, ranging from relationships among the major groups of lice to those among closely related species. Such approaches have also been applied at the population scale in lice, revealing patterns of population subdivision and inbreeding. Finally, whole genome sequence datasets can also be used for additional study beyond that of the louse nuclear genome, such as in the study of mitochondrial genome fragmentation or endosymbiont function. Full article
(This article belongs to the Special Issue Untangling Host-Symbiont Coevolutionary History in the High Throughput Sequencing (HTS) Era)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

 
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