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Sankaranarayanan G, Kodiveri Muthukaliannan G. Exploring antimicrobial resistance determinants in the Neanderthal microbiome. Microbiol Spectr 2024:e0266223. [PMID: 38916350 DOI: 10.1128/spectrum.02662-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/24/2024] [Indexed: 06/26/2024] Open
Abstract
This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history. IMPORTANCE The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.
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Grant AR, Johnson KP, Stanley EL, Baldwin-Brown J, Kolenčík S, Allen JM. Rapid Targeted Assembly of the Proteome Reveals Evolutionary Variation of GC Content in Avian Lice. Bioinform Biol Insights 2024; 18:11779322241257991. [PMID: 38860163 PMCID: PMC11163934 DOI: 10.1177/11779322241257991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/02/2024] [Indexed: 06/12/2024] Open
Abstract
Nucleotide base composition plays an influential role in the molecular mechanisms involved in gene function, phenotype, and amino acid composition. GC content (proportion of guanine and cytosine in DNA sequences) shows a high level of variation within and among species. Many studies measure GC content in a small number of genes, which may not be representative of genome-wide GC variation. One challenge when assembling extensive genomic data sets for these studies is the significant amount of resources (monetary and computational) associated with data processing, and many bioinformatic tools have not been optimized for resource efficiency. Using a high-performance computing (HPC) cluster, we manipulated resources provided to the targeted gene assembly program, automated target restricted assembly method (aTRAM), to determine an optimum way to run the program to maximize resource use. Using our optimum assembly approach, we assembled and measured GC content of all of the protein-coding genes of a diverse group of parasitic feather lice. Of the 499 426 genes assembled across 57 species, feather lice were GC-poor (mean GC = 42.96%) with a significant amount of variation within and between species (GC range = 19.57%-73.33%). We found a significant correlation between GC content and standard deviation per taxon for overall GC and GC3, which could indicate selection for G and C nucleotides in some species. Phylogenetic signal of GC content was detected in both GC and GC3. This research provides a large-scale investigation of GC content in parasitic lice laying the foundation for understanding the basis of variation in base composition across species.
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Affiliation(s)
- Avery R Grant
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Edward L Stanley
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | | | - Stanislav Kolenčík
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Koper, Slovenia
| | - Julie M Allen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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3
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Boyd BM, James I, Johnson KP, Weiss RB, Bush SE, Clayton DH, Dale C. Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria. Nat Commun 2024; 15:4571. [PMID: 38811551 PMCID: PMC11137140 DOI: 10.1038/s41467-024-48784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Evolution results from the interaction of stochastic and deterministic processes that create a web of historical contingency, shaping gene content and organismal function. To understand the scope of this interaction, we examine the relative contributions of stochasticity, determinism, and contingency in shaping gene inactivation in 34 lineages of endosymbiotic bacteria, Sodalis, found in parasitic lice, Columbicola, that are independently undergoing genome degeneration. Here we show that the process of genome degeneration in this system is largely deterministic: genes involved in amino acid biosynthesis are lost while those involved in providing B-vitamins to the host are retained. In contrast, many genes encoding redundant functions, including components of the respiratory chain and DNA repair pathways, are subject to stochastic loss, yielding historical contingencies that constrain subsequent losses. Thus, while selection results in functional convergence between symbiont lineages, stochastic mutations initiate distinct evolutionary trajectories, generating diverse gene inventories that lack the functional redundancy typically found in free-living relatives.
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Affiliation(s)
- Bret M Boyd
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, US.
| | - Ian James
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, US
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, UT, US
| | - Sarah E Bush
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
| | - Colin Dale
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
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Guichard A, Legeai F, Tagu D, Lemaitre C. MTG-Link: leveraging barcode information from linked-reads to assemble specific loci. BMC Bioinformatics 2023; 24:284. [PMID: 37452278 PMCID: PMC10347852 DOI: 10.1186/s12859-023-05395-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. RESULTS We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. CONCLUSIONS MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.
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Affiliation(s)
- Anne Guichard
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France.
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France
| | - Denis Tagu
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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5
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Ke YH, Branco S, Bazzicalupo AL, Nguyen NH, Liao HL, Kennedy P, Bruns TD, Kuo A, LaButti K, Barry K, Grigoriev I, Vilgalys R. Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi. Genetics 2023; 224:iyad069. [PMID: 37070772 PMCID: PMC10213496 DOI: 10.1093/genetics/iyad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 04/19/2023] Open
Abstract
Studying the signatures of evolution can help to understand genetic processes. Here, we demonstrate how the existence of balancing selection can be used to identify the breeding systems of fungi from genomic data. The breeding systems of fungi are controlled by self-incompatibility loci that determine mating types between potential mating partners, resulting in strong balancing selection at the loci. Within the fungal phylum Basidiomycota, two such self-incompatibility loci, namely HD MAT locus and P/R MAT locus, control mating types of gametes. Loss of function at one or both MAT loci results in different breeding systems and relaxes the MAT locus from balancing selection. By investigating the signatures of balancing selection at MAT loci, one can infer a species' breeding system without culture-based studies. Nevertheless, the extreme sequence divergence among MAT alleles imposes challenges for retrieving full variants from both alleles when using the conventional read-mapping method. Therefore, we employed a combination of read-mapping and local de novo assembly to construct haplotypes of HD MAT alleles from genomes in suilloid fungi (genera Suillus and Rhizopogon). Genealogy and pairwise divergence of HD MAT alleles showed that the origins of mating types predate the split between these two closely related genera. High sequence divergence, trans-specific polymorphism, and the deeply diverging genealogy confirm the long-term functionality and multiallelic status of HD MAT locus in suilloid fungi. This work highlights a genomics approach to studying breeding systems regardless of the culturability of organisms based on the interplay between evolution and genetics.
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Affiliation(s)
- Yi-Hong Ke
- Biology Department, Duke University, 130 Science Dr, Durham, NC 27708, USA
| | - Sara Branco
- Integrative Biology, University of Colorado, 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Anna L Bazzicalupo
- Department of Zoology, University of British Columbia, 4200—6270 University Blvd, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Nhu H Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd, Quincy, FL 32351, USA
- Soil and Water Sciences Department, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Thomas D Bruns
- Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Igor Grigoriev
- Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Rytas Vilgalys
- Biology Department, Duke University, 130 Science Dr, Durham, NC 27708, USA
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6
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Galbreath KE, Makarikov AA, Bell KC, Greiman SE, Allen JM, M S Haas G, Li C, Cook JA, Hoberg EP. Late Cenozoic History And The Role Of Beringia In Assembling A Holarctic Cestode Species Complex. Mol Phylogenet Evol 2023; 183:107775. [PMID: 36972794 DOI: 10.1016/j.ympev.2023.107775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/13/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
The dynamic climate history that drove sea level fluctuation during past glacial periods mediated the movement of organisms between Asia and North America via the Bering Land Bridge. Investigations of the biogeographic histories of small mammals and their parasites demonstrate facets of a complex history of episodic geographic colonization and refugial isolation that structured diversity across the Holarctic. We use a large multi-locus nuclear DNA sequence dataset to robustly resolve relationships within the cestode genus Arostrilepis (Cyclophyllidea: Hymenolepididae), a widespread parasite of predominantly arvicoline rodents (voles, lemmings). Using this phylogeny, we confirm that several Asian Arostrilepis lineages colonized North America during up to four distinct glacial periods in association with different rodent hosts, consistent with taxon-pulse dynamics. A previously inferred westward dispersal across the land bridge is rejected. We also refine interpretations of past host colonization, providing evidence for several distinct episodes of expanding host range, which probably contributed to diversification by Arostrilepis. Finally, Arostrilepis is shown to be paraphyletic with respect to Hymenandrya thomomyis, a parasite of pocket gophers, confirming that ancient Arostrilepis species colonized new host lineages upon arriving in North America.
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Affiliation(s)
- Kurt E Galbreath
- Northern Michigan University, 1401, Presque Isle Ave, Marquette, MI 49855.
| | - Arseny A Makarikov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Kayce C Bell
- Natural History Museum of Los Angeles County, 900, Exposition Blvd., Los Angeles, CA 90007
| | - Stephen E Greiman
- Department of Biology, Georgia Southern University, Statesboro, GA 30458
| | - Julie M Allen
- Biology Department, University of Nevada, Reno, Reno, NV 89557
| | - Genevieve M S Haas
- Northern Michigan University, 1401, Presque Isle Ave, Marquette, MI 49855
| | - Chenhong Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, People's Republic of China
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Eric P Hoberg
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
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7
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Reynolds NK, Stajich JE, Benny GL, Barry K, Mondo S, LaButti K, Lipzen A, Daum C, Grigoriev IV, Ho HM, Crous PW, Spatafora JW, Smith ME. Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi. Genome Biol Evol 2023; 15:evac185. [PMID: 36617272 PMCID: PMC9866270 DOI: 10.1093/gbe/evac185] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023] Open
Abstract
Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.
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Affiliation(s)
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California–Riverside
| | | | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Stephen Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
- Department of Plant and Microbial Biology, University of California Berkeley
| | - Hsiao-Man Ho
- Department of Science Education, University of Education, 134, Section 2, Heping E. Road, National Taipei, Taipei 106, Taiwan
| | - Pedro W Crous
- Department of Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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8
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Beckman EJ, Vargas Campos W, Benham PM, Schmitt CJ, Cheviron ZA, Witt CC. Selection on embryonic haemoglobin in an elevational generalist songbird. Biol Lett 2022; 18:20220105. [PMCID: PMC9554719 DOI: 10.1098/rsbl.2022.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Animals developing at high elevation experience a suite of environmental challenges, most notably the low partial pressure of oxygen (PO2) in ambient air. In low PO2, bird species with high-elevation ancestry consistently demonstrate higher hatching success than lowland counterparts, suggesting highland birds are adapted to restricted O2 (hypoxia) in early development. Haemoglobin (Hb), the critical oxygen-transport protein, is a likely target of PO2-related selection across ontogeny since Hb isoforms expressed at distinct developmental stages demonstrate different O2 affinities. To test if Hb function is under PO2-related selection at different ontogenetic stages, we sampled a songbird, the hooded siskin (Spinus magellanicus), across two approximately 4000 m elevational transects. We sequenced all of the loci that encode avian Hb isoforms, and tested for signatures of spatially varying selection by comparing divergence patterns in Hb loci to other loci sampled across the genome. We found strong signatures of diversifying selection at non-synonymous sites in loci that contribute to embryonic (απ, βH) and definitive (βA) Hb isoforms. This is the first evidence for selection on embryonic haemoglobin in high-elevation Neoaves. We conclude that selection on Hb function at brief, but critical stages of ontogeny may be a vital component to high elevation adaptation in birds.
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Affiliation(s)
- Elizabeth J. Beckman
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA,Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Walter Vargas Campos
- Centro de Ornitología y Biodiversidad, Calle Sta. Rita 105, Oficina 202, Santiago de Surco, Lima, Perú
| | - Phred M. Benham
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA,Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - C. Jonathan Schmitt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | | | - Christopher C. Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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9
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Johnson KP. Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice. Life (Basel) 2022; 12:life12091442. [PMID: 36143478 PMCID: PMC9501036 DOI: 10.3390/life12091442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary New sequencing technologies have now made it possible to sequence entire genomes for a diversity of life on earth. Parasites comprise nearly half of all species. Lice are one important group of parasites of birds and mammals, including humans. Genome sequencing approaches have been applied to this group of parasites to uncover patterns of diversification. These patterns can be compared to the patterns of diversification in their hosts. Key findings from these studies have revealed that parasitic lice likely originated on birds and then switched to mammals multiple times. Within groups of birds and mammals, the evolutionary trees of lice match those for mammal hosts more than those for birds. Genomic approaches have also revealed that individual birds and mammals harbor distinct populations of lice. Thus, these new techniques allow for the study of patterns of diversification at a wide variety of scales. 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 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.
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Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
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10
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Virrueta Herrera S, Johnson KP, Sweet AD, Ylinen E, Kunnasranta M, Nyman T. High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal. Mol Ecol 2022; 31:4593-4606. [PMID: 35726520 PMCID: PMC9544963 DOI: 10.1111/mec.16569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 02/02/2023]
Abstract
Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland, and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.
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Affiliation(s)
- Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, Illinois, USA.,Program in Ecology, Evolution, and Conservation, University of Illinois, Urbana, Illinois, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, Illinois, USA
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
| | - Eeva Ylinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
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11
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de Moya RS. Phylogenomics and host-switching patterns of philopteridae (Psocodea: phthiraptera) feather lice. Int J Parasitol 2022; 52:525-537. [DOI: 10.1016/j.ijpara.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 11/05/2022]
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12
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Crane CF, Nemacheck JA, Subramanyam S, Williams CE, Goodwin SB. SLAG: A Program for Seeded Local Assembly of Genes in Complex Genomes. Mol Ecol Resour 2022; 22:1999-2017. [PMID: 34995394 PMCID: PMC9303413 DOI: 10.1111/1755-0998.13580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/11/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022]
Abstract
Although finished genomes have become more common, there is still a need for assemblies of individual genes or chromosomal regions when only unassembled reads are available. slag (Seeded Local Assembly of Genes) fulfils this need by performing iterative local assembly based on cycles of matching‐read retrieval with blast and assembly with cap3, phrap, spades, canu or unicycler. The target sequence can be nucleotide or protein. Read fragmentation allows slag to use phrap or cap3 to assemble long reads at lower coverage (e.g., 5×) than is possible with canu or unicycler. In simple, nonrepetitive genomes, a slag assembly can cover a whole chromosome, but in complex genomes the growth of target‐matching contigs is limited as additional reads are consumed by consensus contigs consisting of repetitive elements. Apart from genomic complexity, contig length and correctness depend on read length and accuracy. With pyrosequencing or Illumina reads, slag‐assembled contigs are accurate enough to allow design of PCR primers, while contigs assembled from Oxford Nanopore or pre‐HiFi Pacific Biosciences long reads are generally only accurate enough to design baiting sequences for further targeted sequencing. In an application with real reads, slag successfully extended sequences for four wheat genes, which were verified by cloning and Sanger sequencing of overlapping amplicons. slag is a robust alternative to atram2 for local assemblies, especially for read sets with less than 20× coverage. slag is freely available at https://github.com/cfcrane/SLAG.
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Affiliation(s)
- Charles F Crane
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Botany & Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA
| | - Jill A Nemacheck
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
| | - Subhashree Subramanyam
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
| | - Christie E Williams
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA
| | - Stephen B Goodwin
- USDA-Agricultural Research Service, Crop Production & Pest Control Research Unit, Purdue University campus, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA.,Department of Botany & Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA
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13
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Boyd BM, Chevignon G, Patel V, Oliver KM, Strand MR. Evolutionary genomics of APSE: a tailed phage that lysogenically converts the bacterium Hamiltonella defensa into a heritable protective symbiont of aphids. Virol J 2021; 18:219. [PMID: 34758862 PMCID: PMC8579659 DOI: 10.1186/s12985-021-01685-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
Background Most phages infect free-living bacteria but a few have been identified that infect heritable symbionts of insects or other eukaryotes. Heritable symbionts are usually specialized and isolated from other bacteria with little known about the origins of associated phages. Hamiltonella defensa is a heritable bacterial symbiont of aphids that is usually infected by a tailed, double-stranded DNA phage named APSE. Methods We conducted comparative genomic and phylogenetic studies to determine how APSE is related to other phages and prophages. Results Each APSE genome was organized into four modules and two predicted functional units. Gene content and order were near-fully conserved in modules 1 and 2, which encode predicted DNA metabolism genes, and module 4, which encodes predicted virion assembly genes. Gene content of module 3, which contains predicted toxin, holin and lysozyme genes differed among haplotypes. Comparisons to other sequenced phages suggested APSE genomes are mosaics with modules 1 and 2 sharing similarities with Bordetella-Bcep-Xylostella fastidiosa-like podoviruses, module 4 sharing similarities with P22-like podoviruses, and module 3 sharing no similarities with known phages. Comparisons to other sequenced bacterial genomes identified APSE-like elements in other heritable insect symbionts (Arsenophonus spp.) and enteric bacteria in the family Morganellaceae. Conclusions APSEs are most closely related to phage elements in the genus Arsenophonus and other bacteria in the Morganellaceae. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01685-y.
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Affiliation(s)
- Bret M Boyd
- Department of Entomology, University of Georgia Athens, Athens, GA, USA. .,Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA.
| | - Germain Chevignon
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER, La Tremblade, France
| | - Vilas Patel
- Department of Entomology, University of Georgia Athens, Athens, GA, USA
| | - Kerry M Oliver
- Department of Entomology, University of Georgia Athens, Athens, GA, USA
| | - Michael R Strand
- Department of Entomology, University of Georgia Athens, Athens, GA, USA.
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14
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Johnson KP, Weckstein JD, Virrueta Herrera S, Doña J. The interplay between host biogeography and phylogeny in structuring diversification of the feather louse genus Penenirmus. Mol Phylogenet Evol 2021; 165:107297. [PMID: 34438049 DOI: 10.1016/j.ympev.2021.107297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022]
Abstract
Parasite diversification is influenced by many of the same factors that affect speciation of free-living organisms, such as biogeographic barriers. However, the ecology and evolution of the host lineage also has a major impact on parasite speciation. Here we explore the interplay between biogeography and host-association on the pattern of diversification in a group of ectoparasitic lice (Insecta: Phthiraptera: Penenirmus) that feeds on the feathers of woodpeckers, barbets, and honeyguides (Piciformes) and some songbirds (Passeriformes). We use whole genome sequencing of 41 ingroup and 12 outgroup samples to develop a phylogenomic dataset of DNA sequences from a reference set of 2395 single copy ortholog genes, for a total of nearly four million aligned base positions. The phylogenetic trees resulting from both concatenated and gene-tree/species-tree coalescent analyses were nearly identical and highly supported. These trees recovered the genus Penenirmus as monophyletic and identified several major clades, which tended to be associated with one major host group. However, cophylogenetic analysis revealed that host-switching was a prominent process in the diversification of this group. This host-switching generally occurred within single major biogeographic regions. We did, however, find one case in which it appears that a rare dispersal event by a woodpecker lineage from North America to Africa allowed its associated louse to colonize a woodpecker in Africa, even though the woodpecker lineage from North America never became established there.
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Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Jason D Weckstein
- Department of Ornithology, Academy of Natural Sciences of Drexel University and Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, Philadelphia, PA, USA
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA; Program in Ecology, Evolution, and Conservation, University of Illinois, Urbana, IL, USA
| | - Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA; Departamento de Biología Animal, Universidad de Granada, Granada, Spain.
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15
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Smith AD, Kamiński MJ, Kanda K, Sweet AD, Betancourt JL, Holmgren CA, Hempel E, Alberti F, Hofreiter M. Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing. Sci Rep 2021; 11:12635. [PMID: 34135378 PMCID: PMC8209150 DOI: 10.1038/s41598-021-91896-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.
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Affiliation(s)
- Aaron D Smith
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA.
| | - Marcin J Kamiński
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
- Zoological Museum, Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warszawa, Poland
| | - Kojun Kanda
- USDA Systematic Entomology Laboratory, C/O Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Andrew D Sweet
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Arkansas State University, State University, AR, 72467, USA
| | | | - Camille A Holmgren
- Department of Geography and Planning, SUNY Buffalo State College, Buffalo, NY, USA
| | - Elisabeth Hempel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Museum Für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Federica Alberti
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Reiss-Engelhorn-Museen, Mannheim, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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16
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Knyshov A, Gordon ERL, Weirauch C. New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics. PeerJ 2021; 9:e11019. [PMID: 33850647 PMCID: PMC8019319 DOI: 10.7717/peerj.11019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/06/2021] [Indexed: 01/03/2023] Open
Abstract
Despite many bioinformatic solutions for analyzing sequencing data, few options exist for targeted sequence retrieval from whole genomic sequencing (WGS) data with the ultimate goal of generating a phylogeny. Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, which may increase rates of false positive results. Many tools are also difficult to install and may lack adequate user resources. Here, we describe a program that uses freely available similarity search tools to find homologs in assembled WGS data with unparalleled freedom to modify parameters. We evaluate its performance compared to other commonly used bioinformatics tools on two divergent insect species (>200 My) for which annotated genomes exist, and on one large set each of highly conserved and more variable loci. Our software is capable of retrieving orthologs from well-curated or unannotated, low or high depth shotgun, and target capture assemblies as well or better than other software as assessed by recovering the most genes with maximal coverage and with a low rate of false positives throughout all datasets. When assessing this combination of criteria, ALiBaSeq is frequently the best evaluated tool for gathering the most comprehensive and accurate phylogenetic alignments on all types of data tested. The software (implemented in Python), tutorials, and manual are freely available at https://github.com/AlexKnyshov/alibaseq.
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Affiliation(s)
- Alexander Knyshov
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
| | - Eric R L Gordon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Christiane Weirauch
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
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17
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Turner KG, Ostevik KL, Grassa CJ, Rieseberg LH. Genomic Analyses of Phenotypic Differences Between Native and Invasive Populations of Diffuse Knapweed (Centaurea diffusa). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.577635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed [Centaurea diffusa Lam. (Asteraceae)]. To assist with this analysis, we have assembled the first draft genome reference and fully annotated plastome assembly for this species, and one of the first from this large, weedy, genus, which is of major ecological and economic importance. We collected phenotype data from 372 individuals from four native and four invasive populations of C. diffusa grown in a common environment. Using these individuals, we produced reduced-representation genotype-by-sequencing (GBS) libraries and identified 7,058 SNPs. We identify two SNPs associated with leaf width in these populations, a trait which significantly varies between native and invasive populations. In this rosette forming species, increased leaf width is a major component of increased biomass, a common trait in invasive plants correlated with increased fitness. Finally, we use annotations from Arabidopsis thaliana to identify 98 candidate genes that are near the associated SNPs and highlight several good candidates for leaf width variation.
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18
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Bell KC, Allen JM, Johnson KP, Demboski JR, Cook JA. Disentangling lousy relationships: Comparative phylogenomics of two sucking louse lineages parasitizing chipmunks. Mol Phylogenet Evol 2020; 155:106998. [PMID: 33130299 DOI: 10.1016/j.ympev.2020.106998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 11/29/2022]
Abstract
The evolution of obligate parasites is often interpreted in light of their hosts' evolutionary history. An expanded approach is to examine the histories of multiple lineages of parasites that inhabit similar environments on a particular host lineage. Western North American chipmunks (genus Tamias) have a broad distribution, a history of divergence with gene flow, and host two species of sucking lice (Anoplura), Hoplopleura arboricola and Neohaematopinus pacificus. From total genomic sequencing, we obtained sequences of over 1100 loci sampled across the genomes of these lice to compare their evolutionary histories and examine the roles of host association in structuring louse relationships. Within each louse species, clades are largely associated with closely related chipmunk host species. Exceptions to this pattern appear to have a biogeographic component, but differ between the two louse species. Phylogenetic relationships among these major louse clades, in both species, are not congruent with chipmunk relationships. In the context of host associations, each louse lineage has a different evolutionary history, supporting the hypothesis that host-parasite assemblages vary both across the landscape and with the taxa under investigation. In addition, the louse Hoplopleura erratica (parasitizing the eastern Tamias striatus) is embedded within H. arboricola, rendering it paraphyletic. This phylogenetic result, together with comparable divergences within H. arboricola, indicate a need for taxonomic revision. Both host divergence and biogeographic components shape parasite diversification as demonstrated by the distinctive diversification patterns of these two independently evolving lineages that parasitize the same hosts.
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Affiliation(s)
- Kayce C Bell
- Mammalogy Department, Natural History Museum of Los Angeles County, Los Angeles, CA, USA; Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA; Zoology Department, Denver Museum of Nature & Science, Denver, CO, USA.
| | - Julie M Allen
- Department of Biology, University of Nevada Reno, Reno, NV, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - John R Demboski
- Zoology Department, Denver Museum of Nature & Science, Denver, CO, USA
| | - Joseph A Cook
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
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19
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Doña J, Sweet AD, Johnson KP. Comparing rates of introgression in parasitic feather lice with differing dispersal capabilities. Commun Biol 2020; 3:610. [PMID: 33097824 PMCID: PMC7584577 DOI: 10.1038/s42003-020-01345-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/30/2020] [Indexed: 12/14/2022] Open
Abstract
Organisms vary in their dispersal abilities, and these differences can have important biological consequences, such as impacting the likelihood of hybridization events. However, there is still much to learn about the factors influencing hybridization, and specifically how dispersal ability affects the opportunities for hybridization. Here, using the ecological replicate system of dove wing and body lice (Insecta: Phthiraptera), we show that species with higher dispersal abilities exhibited increased genomic signatures of introgression. Specifically, we found a higher proportion of introgressed genomic reads and more reticulated phylogenetic networks in wing lice, the louse group with higher dispersal abilities. Our results are consistent with the hypothesis that differences in dispersal ability might drive the extent of introgression through hybridization. Jorge Doña, Andrew Sweet and Kevin Johnson find that dove lice species with higher dispersal abilities have stronger genomic signatures of introgression. By using sequence data from multiple species of both wing and body lice from the same species of hosts, the authors are able to control for nearly all factors besides dispersal ability, demonstrating the power of this study system.
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Affiliation(s)
- Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816 S. Oak St., Champaign, IL, 61820, USA. .,Departamento de Biología Animal, Universidad de Granada, 18001, Granada, Spain.
| | - Andrew D Sweet
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816 S. Oak St., Champaign, IL, 61820, USA.,Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN, 47907, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816 S. Oak St., Champaign, IL, 61820, USA.
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20
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de Moya RS, Yoshizawa K, Walden KKO, Sweet AD, Dietrich CH, Kevin P J. Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets. Syst Biol 2020; 70:719-738. [PMID: 32979270 DOI: 10.1093/sysbio/syaa075] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and nonparasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and nonparasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.[Illumina; Phthiraptera; Psocoptera; quartet sampling; recoding methods.].
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Affiliation(s)
- Robert S de Moya
- Department of Entomology, University of Illinois Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL 61801, USA.,Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Kazunori Yoshizawa
- Systematic Entomology, School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Andrew D Sweet
- Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN 47907, USA
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Johnson Kevin P
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
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21
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Márquez F, Trovant B, Van der Molen S, Sepúlveda RD, Doña J, Johnson KP, Vierna J. Two evolutionary units on the South American razor clam Ensis macha (Bivalvia: Pharidae): genetic and morphometric evidence. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Folk RA, Sewnath N, Xiang CL, Sinn BT, Guralnick RP. Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae). BMC PLANT BIOLOGY 2020; 20:324. [PMID: 32640989 PMCID: PMC7346412 DOI: 10.1186/s12870-020-02533-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 06/28/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of pseudogenization and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome of Saniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context. RESULTS We find that the plastid genome of Saniculiphyllum has experienced pseudogenization of five genes of the ndh complex (ndhA, ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with an aquatic habit, as well as the surprising pseudogenization of two genes more central to photosynthesis (ccsA and cemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional. CONCLUSIONS Saniculiphyllum appears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, perhaps related to its extreme habitat specialization, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi, Mississippi State, USA.
| | - Neeka Sewnath
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
| | - Brandon T Sinn
- Department of Biology & Earth Science, Otterbein University, Westerville, OH, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
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23
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Leal NC, Campos TL, Rezende AM, Docena C, Mendes-Marques CL, de Sá Cavalcanti FL, Wallau GL, Rocha IV, Cavalcanti CLB, Veras DL, Alves LR, Andrade-Figueiredo M, de Barros MPS, de Almeida AMP, de Morais MMC, Leal-Balbino TC, Xavier DE, de-Melo-Neto OP. Comparative Genomics of Acinetobacter baumannii Clinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes. Front Microbiol 2020; 11:1176. [PMID: 32655514 PMCID: PMC7326025 DOI: 10.3389/fmicb.2020.01176] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic bacterial pathogen infecting immunocompromised patients and has gained attention worldwide due to its increased antimicrobial resistance. Here, we report a comparative whole-genome sequencing and analysis coupled with an assessment of antibiotic resistance of 46 Acinetobacter strains (45 A. baumannii plus one Acinetobacter nosocomialis) originated from five hospitals from the city of Recife, Brazil, between 2010 and 2014. An average of 3,809 genes were identified per genome, although only 2,006 genes were single copy orthologs or core genes conserved across all sequenced strains, with an average of 42 new genes found per strain. We evaluated genetic distance through a phylogenetic analysis and MLST as well as the presence of antibiotic resistance genes, virulence markers and mobile genetic elements (MGE). The phylogenetic analysis recovered distinct monophyletic A. baumannii groups corresponding to five known (ST1, ST15, ST25, ST79, and ST113) and one novel ST (ST881, related to ST1). A large number of ST specific genes were found, with the ST79 strains having the largest number of genes in common that were missing from the other STs. Multiple genes associated with resistance to β-lactams, aminoglycosides and other antibiotics were found. Some of those were clearly mapped to defined MGEs and an analysis of those revealed known elements as well as a novel Tn7-Tn3 transposon with a clear ST specific distribution. An association of selected resistance/virulence markers with specific STs was indeed observed, as well as the recent spread of the OXA-253 carbapenemase encoding gene. Virulence genes associated with the synthesis of the capsular antigens were noticeably more variable in the ST113 and ST79 strains. Indeed, several resistance and virulence genes were common to the ST79 and ST113 strains only, despite a greater genetic distance between them, suggesting common means of genetic exchange. Our comparative analysis reveals the spread of multiple STs and the genomic plasticity of A. baumannii from different hospitals in a single metropolitan area. It also highlights differences in the spread of resistance markers and other MGEs between the investigated STs, impacting on the monitoring and treatment of Acinetobacter in the ongoing and future outbreaks.
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Affiliation(s)
- Nilma C Leal
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Túlio L Campos
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Antonio M Rezende
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Cássia Docena
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | | | - Felipe L de Sá Cavalcanti
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil.,Department of Pathology, Institute of Biological Sciences, University of Pernambuco, Recife, Brazil
| | - Gabriel L Wallau
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Igor V Rocha
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | | | - Dyana L Veras
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Lilian R Alves
- Department of Tropical Medicine, Federal University of Pernambuco, Recife, Brazil
| | | | | | | | | | | | - Danilo E Xavier
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
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24
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Virrueta Herrera S, Sweet AD, Allen JM, Walden KKO, Weckstein JD, Johnson KP. Extensive in situ radiation of feather lice on tinamous. Proc Biol Sci 2020; 287:20193005. [PMID: 32070251 PMCID: PMC7062024 DOI: 10.1098/rspb.2019.3005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 01/23/2020] [Indexed: 11/12/2022] Open
Abstract
Tinamous host the highest generic diversity of lice of any group of birds, as well as hosting representatives of all four avian feather louse ecomorphs. Although the generic diversity of tinamou feather lice is well documented, few attempts have been made to reconstruct the phylogenetic relationships among these lice. To test whether tinamou feather lice form a monophyletic group as a whole, we used whole-genome sequencing to estimate a higher-level phylogeny of tinamou feather lice, together with a broad diversity of other avian feather louse groups. In total, we analysed sequences from over 1000 genes for 48 genera of avian lice using both concatenated and coalescent approaches to estimate the phylogeny of this diverse group of avian feather lice. Although the body louse ecomorph of tinamou feather lice formed a monophyletic group, they did not strictly form a monophyletic group together with the other three ecomorphs of tinamou feather lice. In particular, a clade comprised of several feather louse genera, mainly from South America, is nested phylogenetically within tinamou lice, which also have their main centre of diversity in South America. These results suggest in situ radiation of these parasites in South America.
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Affiliation(s)
- Stephany Virrueta Herrera
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Andrew D. Sweet
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | | | | | - Jason D. Weckstein
- Department of Ornithology, Academy of Natural Sciences of Drexel University, and Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, Philadelphia, PA, USA
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
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25
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Johnson KP. Putting the genome in insect phylogenomics. CURRENT OPINION IN INSECT SCIENCE 2019; 36:111-117. [PMID: 31546095 DOI: 10.1016/j.cois.2019.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/02/2019] [Accepted: 08/07/2019] [Indexed: 06/10/2023]
Abstract
Next-generation sequencing technologies provide a substantial increase in the size of molecular phylogenetic datasets that can be obtained for studies of insect systematics. Several new genome reduction approaches are leveraging these technologies to generate large phylogenomic datasets: targeted amplicon sequencing, target capture, and transcriptome sequencing. Although cost effective, these approaches provide limited data for questions outside of phylogenetics. For many groups of insects, sequencing the entire genome at modest coverage is feasible. Using these genomic reads, an automated Target Restricted Assembly Method (aTRAM) can use the results of blast searches to assemble thousands of single copy ortholog genes across a group of interest. These locally assembled genes can then be compiled into very large phylogenomic datasets. These genomic libraries have the advantage in that they also contain reads from the mitochondrial genome and symbiont genomes, as well the entire insect genome, and can be leveraged for additional studies beyond phylogenetics.
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Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820 USA.
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26
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de Moya RS, Allen JM, Sweet AD, Walden KKO, Palma RL, Smith VS, Cameron SL, Valim MP, Galloway TD, Weckstein JD, Johnson KP. Extensive host-switching of avian feather lice following the Cretaceous-Paleogene mass extinction event. Commun Biol 2019; 2:445. [PMID: 31815200 PMCID: PMC6884534 DOI: 10.1038/s42003-019-0689-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/08/2019] [Indexed: 01/08/2023] Open
Abstract
Nearly all lineages of birds host parasitic feather lice. Based on recent phylogenomic studies, the three major lineages of modern birds diverged from each other before the Cretaceous-Paleogene (K-Pg) mass extinction event. In contrast, studies of the phylogeny of feather lice on birds, indicate that these parasites diversified largely after this event. However, these studies were unable to reconstruct the ancestral avian host lineage for feather lice. Here we use genome sequences of a broad diversity of lice to reconstruct a phylogeny based on 1,075 genes. By comparing this louse evolutionary tree to the avian host tree, we show that feather lice began diversifying on the common ancestor of waterfowl and landfowl, then radiated onto other avian lineages by extensive host-switching. Dating analyses and cophylogenetic comparisons revealed that two of three lineages of birds that diverged before the K-Pg boundary acquired their feather lice after this event via host-switching.
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Affiliation(s)
- Robert S. de Moya
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL USA
- Department of Entomology, University of Illinois, Urbana, IL USA
| | - Julie M. Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL USA
- Department of Biology, University of Nevada, Reno, NV USA
| | - Andrew D. Sweet
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL USA
- Department of Entomology, Purdue University, West Lafayette, IN USA
| | | | - Ricardo L. Palma
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Vincent S. Smith
- Department of Life Sciences, The Natural History Museum, London, UK
| | | | | | - Terry D. Galloway
- Department of Entomology, University of Manitoba, Winnipeg, Manitoba Canada
| | - Jason D. Weckstein
- Department of Ornithology, Academy of Natural Sciences of Drexel University, Philadelphia, PA USA
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL USA
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27
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Debray K, Marie-Magdelaine J, Ruttink T, Clotault J, Foucher F, Malécot V. Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae). BMC Evol Biol 2019; 19:152. [PMID: 31340752 PMCID: PMC6657147 DOI: 10.1186/s12862-019-1479-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus. RESULTS We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa. CONCLUSIONS With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks.
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Affiliation(s)
- Kevin Debray
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| | | | - Tom Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Valéry Malécot
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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28
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Rey C, Veber P, Boussau B, Sémon M. CAARS: comparative assembly and annotation of RNA-Seq data. Bioinformatics 2019; 35:2199-2207. [PMID: 30452539 PMCID: PMC6596894 DOI: 10.1093/bioinformatics/bty903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/13/2018] [Accepted: 11/16/2018] [Indexed: 02/05/2023] Open
Abstract
MOTIVATION RNA sequencing (RNA-Seq) is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction. RESULTS We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments. RNA-Seq reads are assembled into transcripts by both de novo and assisted assemblies. Then, CAARS incorporates transcripts into gene families, builds gene alignments and trees and uses phylogenetic information to classify the genes as orthologs and paralogs of existing genes. We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis. We showed CAARS assemblies are more complete and accurate than those assembled by a standard pipeline consisting of de novo assembly coupled with annotation by sequence similarity on a guide species. In addition to annotated transcripts, CAARS provides gene family alignments and trees, annotated with orthology relationships, directly usable for downstream comparative analyses. AVAILABILITY AND IMPLEMENTATION CAARS is implemented in Python and Ocaml and is freely available at https://github.com/carinerey/caars. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Carine Rey
- UnivLyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS UMR, INSERM U1210, LBMC, F-69007, Lyon, France
| | - Philippe Veber
- UnivLyon, Université Claude Bernard Lyon 1, CNRS, UMR, LBBE, F-69100, Villeurbanne, France
| | - Bastien Boussau
- UnivLyon, Université Claude Bernard Lyon 1, CNRS, UMR, LBBE, F-69100, Villeurbanne, France
| | - Marie Sémon
- UnivLyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS UMR, INSERM U1210, LBMC, F-69007, Lyon, France
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29
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Langdon QK, Peris D, Kyle B, Hittinger CT. sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing. Mol Biol Evol 2019; 35:2835-2849. [PMID: 30184140 PMCID: PMC6231485 DOI: 10.1093/molbev/msy166] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and pure species, that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication. As a proof-of-concept, we use the genus Saccharomyces to detect and visualize both interspecies hybrids and pure strains, even with missing parental reference genomes. Through simulation, we show that sppIDer is robust to variable reference genome qualities and performs well with low-coverage data. We further demonstrate the power of this approach in plants, animals, and other fungi. sppIDer is robust to many different inputs and provides visually intuitive insight into genome composition that enables the rapid identification of species and their interspecies hybrids. sppIDer exists as a Docker image, which is a reusable, reproducible, transparent, and simple-to-run package that automates the pipeline and installation of the required dependencies (https://github.com/GLBRC/sppIDer; last accessed September 6, 2018).
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Affiliation(s)
- Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI.,Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI
| | - David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI.,Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI.,Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Brian Kyle
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI.,Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
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30
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Johnson KP, Nguyen NP, Sweet AD, Boyd BM, Warnow T, Allen JM. Simultaneous radiation of bird and mammal lice following the K-Pg boundary. Biol Lett 2019; 14:rsbl.2018.0141. [PMID: 29794007 DOI: 10.1098/rsbl.2018.0141] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/27/2018] [Indexed: 12/30/2022] Open
Abstract
The diversification of parasite groups often occurs at the same time as the diversification of their hosts. However, most studies demonstrating this concordance only examine single host-parasite groups. Multiple diverse lineages of ectoparasitic lice occur across both birds and mammals. Here, we describe the evolutionary history of lice based on analyses of 1107 single-copy orthologous genes from sequenced genomes of 46 species of lice. We identify three major diverse groups of lice: one exclusively on mammals, one almost exclusively on birds and one on both birds and mammals. Each of these groups radiated just after the Cretaceous-Paleogene (K-Pg) boundary, the time of the mass extinction event of the dinosaurs and rapid diversification of most of the modern lineages of birds and mammals.
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Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Nam-Phuong Nguyen
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrew D Sweet
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA.,Program in Ecology, Evolution, and Conservation Biology, School of Integrative Biology, University of Illinois, Urbana, IL 61801, USA
| | - Bret M Boyd
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA.,Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois, Urbana, IL 61801, USA.,Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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31
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Rates of niche and phenotype evolution lag behind diversification in a temperate radiation. Proc Natl Acad Sci U S A 2019; 116:10874-10882. [PMID: 31085636 PMCID: PMC6561174 DOI: 10.1073/pnas.1817999116] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Alternative models of evolutionary processes suggest different associations between species diversification and trait evolution, but limited empirical evidence is available to test these models across large clades at global extents. Here we investigate the relative timing of species diversification and niche and phenotypic evolution across a global plant radiation (Saxifragales) with enormous phenotypic and habitat variation. We demonstrate strong temporal lags among rates, with increased diversification occurring first, followed by niche and phenotype. Accelerated diversification rates are coincident with mid-Miocene expansion of temperate biomes. Later increases in niche and phenotypic evolutionary rates argue against density-dependent diversification alone, indicating a major role for ecological opportunity. These results have broad implications for understanding diversification processes and the origin of present-day temperate biotas. Environmental change can create opportunities for increased rates of lineage diversification, but continued species accumulation has been hypothesized to lead to slowdowns via competitive exclusion and niche partitioning. Such density-dependent models imply tight linkages between diversification and trait evolution, but there are plausible alternative models. Little is known about the association between diversification and key ecological and phenotypic traits at broad phylogenetic and spatial scales. Do trait evolutionary rates coincide with rates of diversification, are there lags among these rates, or is diversification niche-neutral? To address these questions, we combine a deeply sampled phylogeny for a major flowering plant clade—Saxifragales—with phenotype and niche data to examine temporal patterns of evolutionary rates. The considerable phenotypic and habitat diversity of Saxifragales is greatest in temperate biomes. Global expansion of these habitats since the mid-Miocene provided ecological opportunities that, with density-dependent adaptive radiation, should result in simultaneous rate increases for diversification, niche, and phenotype, followed by decreases with habitat saturation. Instead, we find that these rates have significantly different timings, with increases in diversification occurring at the mid-Miocene Climatic Optimum (∼15 Mya), followed by increases in niche and phenotypic evolutionary rates by ∼5 Mya; all rates increase exponentially to the present. We attribute this surprising lack of temporal coincidence to initial niche-neutral diversification followed by ecological and phenotypic divergence coincident with more extreme cold and dry habitats that proliferated into the Pleistocene. A lack of density-dependence contrasts with investigations of other cosmopolitan lineages, suggesting alternative patterns may be common in the diversification of temperate lineages.
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32
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Allio R, Scornavacca C, Nabholz B, Clamens AL, Sperling FAH, Condamine FL. Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution. Syst Biol 2019; 69:38-60. [DOI: 10.1093/sysbio/syz030] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 01/20/2023] Open
Abstract
Abstract
Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous nonbiological models in parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies—swallowtails of the family Papilionidae—that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced data set (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 Ma (95% credibility interval: 68.6–142.7 Ma) and Papilionidae around 71.4 Ma (49.8–103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Céline Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Institut de Biologie Computationnelle (IBC), Montpellier, France
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Anne-Laure Clamens
- INRA, UMR 1062 Centre de Biologie pour la Gestion des Populations (INRA, IRD, CIRAD, Montpellier SupAgro), 755 Avenue du Campus Agropolis, 34988 Montferrier-sur-Lez, France
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Felix AH Sperling
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Fabien L Condamine
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
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33
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Barrow LN, Allen JM, Huang X, Bensch S, Witt CC. Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host-parasite evolution. Mol Ecol Resour 2019; 19:400-410. [PMID: 30554480 DOI: 10.1111/1755-0998.12977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 12/27/2022]
Abstract
Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus and Leucocytoozoon) represent an exciting multihost, multiparasite system in ecology and evolution. Global research in this field accelerated after the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode and the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing the transition to genomic-scale sequencing techniques. We extend a recently developed sequence capture method to obtain hundreds of haemosporidian nuclear loci from wild bird samples, which typically have low levels of infection, or parasitemia. We tested 51 infected birds from Peru and New Mexico and evaluated locus recovery in light of variation in parasitemia, divergence from reference sequences and pooling strategies. Our method was successful for samples with parasitemia as low as ~0.02% (2 of 10,000 blood cells infected) and mtDNA divergence as high as 15.9% (one Leucocytozoonsample), and using the most cost-effective pooling strategy tested. Phylogenetic relationships estimated with >300 nuclear loci were well resolved, providing substantial improvement over the mtDNA barcode. We provide protocols for sample preparation and sequence capture including custom probe sequences and describe our bioinformatics pipeline using atram 2.0, phyluce and custom Perl/Python scripts. This approach can be applied to thousands of avian samples that have already been found to have haemosporidian infections of at least moderate intensity, greatly improving our understanding of parasite speciation, biogeography and evolutionary dynamics.
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Affiliation(s)
- Lisa N Barrow
- Museum of Southwestern Biology and Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, New Mexico
| | - Julie M Allen
- Department of Biology, University of Nevada, Reno, Nevada
| | - Xi Huang
- Department of Biology, Molecular Ecology and Evolution Laboratory, Lund University, Lund, Sweden
| | - Staffan Bensch
- Department of Biology, Molecular Ecology and Evolution Laboratory, Lund University, Lund, Sweden
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, New Mexico
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34
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Zhang F, Ding Y, Zhu C, Zhou X, Orr MC, Scheu S, Luan Y. Phylogenomics from low‐coverage whole‐genome sequencing. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13145] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Feng Zhang
- Department of EntomologyCollege of Plant ProtectionNanjing Agricultural University Nanjing P. R. China
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of Sciences Beijing P. R. China
- J. F. Blumenbach Institute of Zoology and AnthropologyUniversity of Göttingen Göttingen Germany
| | - Yinhuan Ding
- Department of EntomologyCollege of Plant ProtectionNanjing Agricultural University Nanjing P. R. China
| | - Chao‐Dong Zhu
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of Sciences Beijing P. R. China
- College of Life SciencesUniversity of Chinese Academy of Sciences Beijing P. R. China
| | - Xin Zhou
- Department of EntomologyChina Agricultural University Beijing P. R. China
| | - Michael C. Orr
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of Sciences Beijing P. R. China
| | - Stefan Scheu
- J. F. Blumenbach Institute of Zoology and AnthropologyUniversity of Göttingen Göttingen Germany
| | - Yun‐Xia Luan
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied TechnologyInstitute of Insect Science and TechnologySchool of Life SciencesSouth China Normal University Guangzhou P. R. China
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35
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White DM, Islam MB, Mason-Gamer RJ. Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species). AMERICAN JOURNAL OF BOTANY 2019; 106:154-165. [PMID: 30629286 DOI: 10.1002/ajb2.1224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/19/2018] [Indexed: 05/12/2023]
Abstract
PREMISE OF THE STUDY This investigation establishes the first DNA-sequence-based phylogenetic hypothesis of species relationships in the coca family (Erythroxylaceae) and presents its implications for the intrageneric taxonomy and neotropical biogeography of Erythroxylum. We also identify the closest wild relatives and evolutionary relationships of the cultivated coca taxa. METHODS We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O.E.Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. KEY RESULTS We show that neotropical Erythroxylum are monophyletic within the paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipes and E. cataractarum are most closely related to the cultivated E. coca and E. novogranatense, but relationships within this "coca" clade remain equivocal. CONCLUSIONS Our results point to the difficulty of morphology-based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. We can confidently identify E. gracilipes and E. cataractarum as the closest wild relatives of the coca taxa, but understanding the domestication history of this crop will require more thorough phylogeographic analysis.
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Affiliation(s)
- Dawson M White
- Department of Biological Sciences, University of Illinois at Chicago, 845 West Taylor Street Room 3256 (M/C 066), Chicago, IL, 60612, USA
- Department of Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - Melissa B Islam
- Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N122, Campus Box 334, Boulder, CO, 80309, USA
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, 845 West Taylor Street Room 3256 (M/C 066), Chicago, IL, 60612, USA
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36
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Sweet AD, Johnson KP. The role of parasite dispersal in shaping a host–parasite system at multiple evolutionary scales. Mol Ecol 2018; 27:5104-5119. [DOI: 10.1111/mec.14937] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/13/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Andrew D. Sweet
- Illinois Natural History Survey, Prairie Research Institute University of Illinois at Urbana‐Champaign Champaign Illinois
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute University of Illinois at Urbana‐Champaign Champaign Illinois
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37
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Singh KS, Beadle K, Troczka BJ, Field L, Davies E, Williamson M, Nauen R, Bass C. Extension of Partial Gene Transcripts by Iterative Mapping of RNA-Seq Raw Reads. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 16:1036-1041. [PMID: 30106739 DOI: 10.1109/tcbb.2018.2865309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many non-model organisms lack reference genomes and the sequencing and de novo assembly of an organism's transcriptome is an affordable means by which to characterize the coding component of its genome. Despite the advances that have made this possible, assembling a transcriptome without a known reference usually results in a collection of full-length and partial gene transcripts. The downstream analysis of genes represented as partial transcripts then often requires further experimental work in the laboratory in order to obtain full- length sequences. We have explored whether partial transcripts, encoding genes of interest present in de novo assembled transcriptomes of a model and non-model insect species, could be further extended by iterative mapping against the raw transcriptome sequencing reads. Partial sequences encoding cytochrome P450s and carboxyl/cholinesterase were used in this analysis because they are large multigene families and exhibit significant variation in expression. We present an effective method to improve the continuity of partial transcripts in silico that, in the absence of a reference genome, maybe a quick and cost-effective alternative to their extension by laboratory experimentation. Our approach resulted in the successful extension of incompletely assembled transcripts, often to full length. We experimentally validated these results \textit{in silico} and using real-time PCR and sequencing.
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38
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Herrando-Moraira S. Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae). Mol Phylogenet Evol 2018; 128:69-87. [PMID: 30036700 DOI: 10.1016/j.ympev.2018.07.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/17/2022]
Abstract
Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue with an ultimate goal to shed light into a highly diversified group of Compositae (Asteraceae) constituted by four main genera: Arctium, Cousinia, Saussurea, and Jurinea. Specifically, we compared sequence data extraction methods implemented in two easy-to-use workflows, PHYLUCE and HybPiper, and assessed the impact of two filtering practices intended to reduce phylogenetic noise. In addition, we compared two phylogenetic inference methods: (1) the concatenation approach, in which all loci were concatenated in a supermatrix; and (2) the coalescence approach, in which gene trees were produced independently and then used to construct a species tree under coalescence assumptions. Here we confirm the usefulness of the set of 1061 COS targets (a nuclear conserved orthology loci set developed for the Compositae) across a variety of taxonomic levels. Intergeneric relationships were completely resolved: there are two sister groups, Arctium-Cousinia and Saussurea-Jurinea, which are in agreement with a morphological hypothesis. Intrageneric relationships among species of Arctium, Cousinia, and Saussurea are also well defined. Conversely, conflicting species relationships remain for Jurinea. Methodological choices significantly affected phylogenies in terms of topology, branch length, and support. Across all analyses, the phylogeny obtained using HybPiper and the strictest scheme of removing fast-evolving sites was estimated as the optimal. Regarding methodological choices, we conclude that: (1) trees obtained under the coalescence approach are topologically more congruent between them than those inferred using the concatenation approach; (2) refining treatments only improved support values under the concatenation approach; and (3) branch support values are maximized when fast-evolving sites are removed in the concatenation approach, and when a higher number of loci is analyzed in the coalescence approach.
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Affiliation(s)
- Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s.n., 08038 Barcelona, Spain.
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39
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Allen JM, LaFrance R, Folk RA, Johnson KP, Guralnick RP. aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data. Evol Bioinform Online 2018; 14:1176934318774546. [PMID: 29881251 PMCID: PMC5987885 DOI: 10.1177/1176934318774546] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/09/2018] [Indexed: 11/17/2022] Open
Abstract
Massive strides have been made in technologies for collecting genome-scale data. However, tools for efficiently and flexibly assembling raw outputs into downstream analytical workflows are still nascent. aTRAM 1.0 was designed to assemble any locus from genome sequencing data but was neither optimized for efficiency nor able to serve as a single toolkit for all assembly needs. We have completely re-implemented aTRAM and redesigned its structure for faster read retrieval while adding a number of key features to improve flexibility and functionality. The software can now (1) assemble single- or paired-end data, (2) utilize both read directions in the database, (3) use an additional de novo assembly module, and (4) leverage new built-in pipelines to automate common workflows in phylogenomics. Owing to reimplementation of databasing strategies, we demonstrate that aTRAM 2.0 is much faster across all applications compared to the previous version.
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Affiliation(s)
- Julie M Allen
- Florida Museum of Natural History and University of Florida, Gainesville, FL, USA
| | - Raphael LaFrance
- Florida Museum of Natural History and University of Florida, Gainesville, FL, USA
| | - Ryan A Folk
- Florida Museum of Natural History and University of Florida, Gainesville, FL, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Robert P Guralnick
- Florida Museum of Natural History and University of Florida, Gainesville, FL, USA
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40
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Kucuk E, Chu J, Vandervalk BP, Hammond SA, Warren RL, Birol I. Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinformatics 2018; 33:1782-1788. [PMID: 28186221 PMCID: PMC5572715 DOI: 10.1093/bioinformatics/btx078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Despite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of computational resources and expertise. A targeted assembly approach to perform local assembly of sequences of interest remains a valuable option for some applications. This is especially true for gene-centric assemblies, whose resulting sequence can be readily utilized for more focused biological research. Here we describe Kollector, an alignment-free targeted assembly pipeline that uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector robustly reconstructs introns and novel sequences within these loci, and scales well to large genomes—properties that makes it especially useful for researchers working on non-model eukaryotic organisms. Results We demonstrate the performance of Kollector for assembling complete or near-complete Caenorhabditis elegans and Homo sapiens gene loci from their respective, input transcripts. In a time- and memory-efficient manner, the Kollector pipeline successfully reconstructs respectively 99% and 80% (compared to 86% and 73% with standard de novo assembly techniques) of C.elegans and H.sapiens transcript targets in their corresponding genomic space using whole genome shotgun sequencing reads. We also show that Kollector outperforms both established and recently released targeted assembly tools. Finally, we demonstrate three use cases for Kollector, including comparative and cancer genomics applications. Availability and Implementation Kollector is implemented as a bash script, and is available at https://github.com/bcgsc/kollector Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erdi Kucuk
- University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Justin Chu
- University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Benjamin P Vandervalk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Inanc Birol
- University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.,Simon Fraser University, Burnaby, BC, Canada
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41
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Mitochondrial phylogenomics and genome rearrangements in the barklice (Insecta: Psocodea). Mol Phylogenet Evol 2018; 119:118-127. [DOI: 10.1016/j.ympev.2017.10.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 11/19/2022]
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42
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Esin A, Bergendahl LT, Savolainen V, Marsh JA, Warnecke T. The genetic basis and evolution of red blood cell sickling in deer. Nat Ecol Evol 2018; 2:367-376. [PMID: 29255300 PMCID: PMC5777626 DOI: 10.1038/s41559-017-0420-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/20/2017] [Indexed: 11/09/2022]
Abstract
Crescent-shaped red blood cells, the hallmark of sickle-cell disease, present a striking departure from the biconcave disc shape normally found in mammals. Characterized by increased mechanical fragility, sickled cells promote haemolytic anaemia and vaso-occlusions and contribute directly to disease in humans. Remarkably, a similar sickle-shaped morphology has been observed in erythrocytes from several deer species, without obvious pathological consequences. The genetic basis of erythrocyte sickling in deer, however, remains unknown. Here, we determine the sequences of human β-globin orthologues in 15 deer species and use protein structural modelling to identify a sickling mechanism distinct from the human disease, coordinated by a derived valine (E22V) that is unique to sickling deer. Evidence for long-term maintenance of a trans-species sickling/non-sickling polymorphism suggests that sickling in deer is adaptive. Our results have implications for understanding the ecological regimes and molecular architectures that have promoted convergent evolution of sickling erythrocytes across vertebrates.
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Affiliation(s)
- Alexander Esin
- Molecular Systems Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, United Kingdom
| | - L Therese Bergendahl
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
- University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Joseph A Marsh
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Tobias Warnecke
- Molecular Systems Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, United Kingdom.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, United Kingdom.
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43
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Sweet AD, Boyd BM, Allen JM, Villa SM, Valim MP, Rivera-Parra JL, Wilson RE, Johnson KP. Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution. Evolution 2017; 72:95-112. [PMID: 29094340 DOI: 10.1111/evo.13386] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/12/2017] [Accepted: 10/23/2017] [Indexed: 02/05/2023]
Abstract
Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g., cospeciation, host switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice. By comparing the louse and ground-dove phylogenies, we found that over long-term evolutionary scales their phylogenies were largely congruent. Many louse lineages (both species and populations) also demonstrated high host-specificity, suggesting ground-dove divergence is a primary driver of their parasites' diversity. However, the few louse taxa that are generalists are structured according to biogeography at the population level. This suggests dispersal among sympatric hosts has some effect on body louse diversity, but over deeper time scales the parasites eventually sort according to host species. Overall, our results demonstrate that multiple factors explain the patterns of diversity in this group of parasites, and that the effects of these factors can vary over different evolutionary scales. The integrative approach we employed was crucial for uncovering these patterns, and should be broadly applicable to other studies.
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Affiliation(s)
- Andrew D Sweet
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820.,Program in Ecology, Evolution, and Conservation Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820
| | - Bret M Boyd
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820.,Department of Entomology, University of Georgia, Athens, Georgia 30602
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820.,Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Scott M Villa
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Michel P Valim
- Biotério da Universidade Iguaçu, Av. Abílio Augusto Távora, 2134, RJ 26275, Brazil
| | - Jose L Rivera-Parra
- Departamento de Petroleos, Facultad de Geologia y Petroleos, Escuela Politecnica Nacional, Quito, Ecuador
| | - Robert E Wilson
- Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820
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44
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Boyd BM, Allen JM, Nguyen NP, Sweet AD, Warnow T, Shapiro MD, Villa SM, Bush SE, Clayton DH, Johnson KP. Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola). Syst Biol 2017; 66:896-911. [PMID: 28108601 PMCID: PMC5837638 DOI: 10.1093/sysbio/syx027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/30/2016] [Accepted: 01/06/2017] [Indexed: 01/01/2023] Open
Abstract
Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species. Understanding the ecological and evolutionary factors that influence coadaptation and codiversification in this system will substantially improve our understanding of coevolution in general. However, further work is hampered by the lack of a robust phylogenetic framework for Columbicola spp. and their hosts. Previous attempts to resolve the phylogeny of Columbicola based on sequences from a few genes provided limited support. Here, we apply a new approach, target restricted assembly, to assemble 977 orthologous gene sequences from whole-genome sequence data generated from very small, ethanol-preserved specimens, representing up to 61 species of wing lice. Both concatenation and coalescent methods were used to estimate the species tree. These two approaches yielded consistent and well-supported trees with 90% of all relationships receiving 100% support, which is a substantial improvement over previous studies. We used this new phylogeny to show that biogeographic ranges are generally conserved within clades of Columbicola wing lice. Limited inconsistencies are probably attributable to intercontinental dispersal of hosts, and host switching by some of the lice. [aTRAM; coalescent; coevolution; concatenation; species tree.].
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Affiliation(s)
- Bret M. Boyd
- Department of Entomology, University of Georgia Athens, 413 Biological Sciences Building, Athens, GA 30602, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
| | - Julie M. Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Nam-Phuong Nguyen
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrew D. Sweet
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
| | - Tandy Warnow
- Departments of Computer Science and Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Michael D. Shapiro
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Scott M. Villa
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Sarah E. Bush
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Dale H. Clayton
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
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Boyd BM, Allen JM, Nguyen NP, Vachaspati P, Quicksall ZS, Warnow T, Mugisha L, Johnson KP, Reed DL. Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice. Mol Biol Evol 2017; 34:1743-1757. [PMID: 28419279 PMCID: PMC5455983 DOI: 10.1093/molbev/msx117] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here, we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement. Examination of the highly reduced symbiont genomes (0.53–0.57 Mb) reveals much of the genomes are dedicated to vitamin synthesis. This is unchanged in the smallest symbiont genome and one that appears to have been reorganized. Specifically, symbionts from human lice, chimpanzee lice, and gorilla lice carry a small plasmid that encodes synthesis of vitamin B5, a vitamin critical to the bacteria-louse symbiosis. This plasmid is absent in an old world monkey louse symbiont, where this pathway is on its primary chromosome. This suggests the unique genomic configuration brought about by the plasmid is not essential for symbiosis, but once obtained, it has persisted for up to 25 My. We also find evidence that human, chimpanzee, and gorilla louse endosymbionts have lost a pathway for synthesis of vitamin B1, whereas the monkey louse symbiont has retained this pathway. It is unclear whether these changes are adaptive, but they may point to evolutionary responses of louse symbionts to shifts in primate biology.
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Affiliation(s)
- Bret M Boyd
- Department of Entomology, University of Georgia Athens, Athens, GA.,Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL.,Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Nam-Phuong Nguyen
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA
| | - Pranjal Vachaspati
- Department of Computer Science and Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL
| | | | - Tandy Warnow
- Department of Computer Science and Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL
| | - Lawrence Mugisha
- Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda.,College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL
| | - David L Reed
- Florida Museum of Natural History, University of Florida, Gainesville, FL
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García N, Folk RA, Meerow AW, Chamala S, Gitzendanner MA, Oliveira RSD, Soltis DE, Soltis PS. Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae). Mol Phylogenet Evol 2017; 111:231-247. [PMID: 28390909 DOI: 10.1016/j.ympev.2017.04.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 12/23/2022]
Abstract
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: (1) Tocantinia and Hippeastrum with 2n=22, and (2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n=12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.
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Affiliation(s)
- Nicolás García
- Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Av. Santa Rosa 11315, La Pintana, Santiago, Chile; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
| | - Ryan A Folk
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
| | - Alan W Meerow
- USDA-ARS-SHRS-National Germplasm Repository, 13601 Old Cutler Road, Miami, FL 33158, USA.
| | - Srikar Chamala
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA.
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Renata Souza de Oliveira
- GaTE Laboratory, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, IBUSP, Rua do Matão 277, CEP: 05508-090 São Paulo, SP, Brazil.
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
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Leung MCK, Procter AC, Goldstone JV, Foox J, DeSalle R, Mattingly CJ, Siddall ME, Timme-Laragy AR. Applying evolutionary genetics to developmental toxicology and risk assessment. Reprod Toxicol 2017; 69:174-186. [PMID: 28267574 PMCID: PMC5829367 DOI: 10.1016/j.reprotox.2017.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 12/26/2022]
Abstract
Evolutionary thinking continues to challenge our views on health and disease. Yet, there is a communication gap between evolutionary biologists and toxicologists in recognizing the connections among developmental pathways, high-throughput screening, and birth defects in humans. To increase our capability in identifying potential developmental toxicants in humans, we propose to apply evolutionary genetics to improve the experimental design and data interpretation with various in vitro and whole-organism models. We review five molecular systems of stress response and update 18 consensual cell-cell signaling pathways that are the hallmark for early development, organogenesis, and differentiation; and revisit the principles of teratology in light of recent advances in high-throughput screening, big data techniques, and systems toxicology. Multiscale systems modeling plays an integral role in the evolutionary approach to cross-species extrapolation. Phylogenetic analysis and comparative bioinformatics are both valuable tools in identifying and validating the molecular initiating events that account for adverse developmental outcomes in humans. The discordance of susceptibility between test species and humans (ontogeny) reflects their differences in evolutionary history (phylogeny). This synthesis not only can lead to novel applications in developmental toxicity and risk assessment, but also can pave the way for applying an evo-devo perspective to the study of developmental origins of health and disease.
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Affiliation(s)
- Maxwell C K Leung
- Nicholas School of the Environment, Duke University, Durham, NC, United States.
| | - Andrew C Procter
- Institute for Advanced Analytics, North Carolina State University, Raleigh, NC, United States
| | - Jared V Goldstone
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Jonathan Foox
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
| | - Robert DeSalle
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
| | - Carolyn J Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States
| | - Mark E Siddall
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
| | - Alicia R Timme-Laragy
- Department of Environmental Health Sciences, University of Massachusetts, Amherst, MA, United States
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Hu H, Gu X, Xue LJ, Swamy PS, Harding SA, Tsai CJ. Tubulin C-terminal Post-translational Modifications Do Not Occur in Wood Forming Tissue of Populus. FRONTIERS IN PLANT SCIENCE 2016; 7:1493. [PMID: 27790223 PMCID: PMC5061773 DOI: 10.3389/fpls.2016.01493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/20/2016] [Indexed: 05/03/2023]
Abstract
Cortical microtubules (MTs) are evolutionarily conserved cytoskeletal components with specialized roles in plants, including regulation of cell wall biogenesis. MT functions and dynamics are dictated by the composition of their monomeric subunits, α- (TUA) and β-tubulins (TUB), which in animals and protists are subject to both transcriptional regulation and post-translational modifications (PTM). While spatiotemporal regulation of tubulin gene expression has been reported in plants, whether and to what extent tubulin PTMs occur in these species remain poorly understood. We chose the woody perennial Populus for investigation of tubulin PTMs in this study, with a particular focus on developing xylem where high tubulin transcript levels support MT-dependent secondary cell wall deposition. Mass spectrometry and immunodetection concurred that detyrosination, non-tyrosination and glutamylation were essentially absent in tubulins isolated from wood-forming tissues of P. deltoides and P. tremula ×alba. Label-free quantification of tubulin isotypes and RNA-Seq estimation of tubulin transcript abundance were largely consistent with transcriptional regulation. However, two TUB isotypes were detected at noticeably lower levels than expected based on RNA-Seq transcript abundance in both Populus species. These findings led us to conclude that MT composition during wood formation depends exclusively on transcriptional and, to a lesser extent, translational regulation of tubulin isotypes.
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Affiliation(s)
- Hao Hu
- Daniel B. Warnell School of Forestry and Natural Resources, University of GeorgiaAthens, GA, USA
- Department of Genetics, University of GeorgiaAthens, GA, USA
| | - Xi Gu
- Institute of Bioinformatics, University of GeorgiaAthens, GA, USA
| | - Liang-Jiao Xue
- Daniel B. Warnell School of Forestry and Natural Resources, University of GeorgiaAthens, GA, USA
- Department of Genetics, University of GeorgiaAthens, GA, USA
- Institute of Bioinformatics, University of GeorgiaAthens, GA, USA
| | - Prashant S. Swamy
- Daniel B. Warnell School of Forestry and Natural Resources, University of GeorgiaAthens, GA, USA
| | - Scott A. Harding
- Daniel B. Warnell School of Forestry and Natural Resources, University of GeorgiaAthens, GA, USA
- Department of Genetics, University of GeorgiaAthens, GA, USA
| | - Chung-Jui Tsai
- Daniel B. Warnell School of Forestry and Natural Resources, University of GeorgiaAthens, GA, USA
- Department of Genetics, University of GeorgiaAthens, GA, USA
- Institute of Bioinformatics, University of GeorgiaAthens, GA, USA
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Two Bacterial Genera, Sodalis and Rickettsia, Associated with the Seal Louse Proechinophthirus fluctus (Phthiraptera: Anoplura). Appl Environ Microbiol 2016; 82:3185-97. [PMID: 26994086 PMCID: PMC4959230 DOI: 10.1128/aem.00282-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/14/2016] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Roughly 10% to 15% of insect species host heritable symbiotic bacteria known as endosymbionts. The lice parasitizing mammals rely on endosymbionts to provide essential vitamins absent in their blood meals. Here, we describe two bacterial associates from a louse, Proechinophthirus fluctus, which is an obligate ectoparasite of a marine mammal. One of these is a heritable endosymbiont that is not closely related to endosymbionts of other mammalian lice. Rather, it is more closely related to endosymbionts of the genus Sodalis associated with spittlebugs and feather-chewing bird lice. Localization and vertical transmission of this endosymbiont are also more similar to those of bird lice than to those of other mammalian lice. The endosymbiont genome appears to be degrading in symbiosis; however, it is considerably larger than the genomes of other mammalian louse endosymbionts. These patterns suggest the possibility that this Sodalis endosymbiont might be recently acquired, replacing a now-extinct, ancient endosymbiont. From the same lice, we also identified an abundant bacterium belonging to the genus Rickettsia that is closely related to Rickettsia ricketsii, a human pathogen vectored by ticks. No obvious masses of the Rickettsia bacterium were observed in louse tissues, nor did we find any evidence of vertical transmission, so the nature of its association remains unclear. IMPORTANCE Many insects are host to heritable symbiotic bacteria. These heritable bacteria have been identified from numerous species of parasitic lice. It appears that novel symbioses have formed between lice and bacteria many times, with new bacterial symbionts potentially replacing existing ones. However, little was known about the symbionts of lice parasitizing marine mammals. Here, we identified a heritable bacterial symbiont in lice parasitizing northern fur seals. This bacterial symbiont appears to have been recently acquired by the lice. The findings reported here provide insights into how new symbioses form and how this lifestyle is shaping the symbiont genome.
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Yeates DK, Meusemann K, Trautwein M, Wiegmann B, Zwick A. Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution. CURRENT OPINION IN INSECT SCIENCE 2016; 13:16-23. [PMID: 27436549 DOI: 10.1016/j.cois.2015.10.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/08/2015] [Accepted: 10/18/2015] [Indexed: 06/06/2023]
Abstract
Our understanding on the phylogenetic relationships of insects has been revolutionised in the last decade by the proliferation of next generation sequencing technologies (NGS). NGS has allowed insect systematists to assemble very large molecular datasets that include both model and non-model organisms. Such datasets often include a large proportion of the total number of protein coding sequences available for phylogenetic comparison. We review some early entomological phylogenomic studies that employ a range of different data sampling protocols and analyses strategies, illustrating a fundamental renaissance in our understanding of insect evolution all driven by the genomic revolution. The analysis of phylogenomic datasets is challenging because of their size and complexity, and it is obvious that the increasing size alone does not ensure that phylogenetic signal overcomes systematic biases in the data. Biases can be due to various factors such as the method of data generation and assembly, or intrinsic biological feature of the data per se, such as similarities due to saturation or compositional heterogeneity. Such biases often cause violations in the underlying assumptions of phylogenetic models. We review some of the bioinformatics tools available and being developed to detect and minimise systematic biases in phylogenomic datasets. Phylogenomic-scale data coupled with sophisticated analyses will revolutionise our understanding of insect functional genomics. This will illuminate the relationship between the vast range of insect phenotypic diversity and underlying genetic diversity. In combination with rapidly developing methods to estimate divergence times, these analyses will also provide a compelling view of the rates and patterns of lineagenesis (birth of lineages) over the half billion years of insect evolution.
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Affiliation(s)
- David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia.
| | - Karen Meusemann
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Michelle Trautwein
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Brian Wiegmann
- Department of Entomology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
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