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Najer T, Doña J, Buček A, Sweet AD, Sychra O, Johnson KP. Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution. PLoS Genet 2024; 20:e1011266. [PMID: 38701107 DOI: 10.1371/journal.pgen.1011266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
While mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, many species of parasitic lice (Insecta: Phthiraptera) are among the notable exceptions, having mitogenomes fragmented into multiple circular chromosomes. To better understand the process of mitogenome fragmentation, we conducted a large-scale genomic study of a major group of lice, Amblycera, with extensive taxon sampling. Analyses of the evolution of mitogenome structure across a phylogenomic tree of 90 samples from 53 genera revealed evidence for multiple independent origins of mitogenome fragmentation, some inferred to have occurred less than five million years ago. We leveraged these many independent origins of fragmentation to compare the rates of DNA substitution and gene rearrangement, specifically contrasting branches with fragmented and non-fragmented mitogenomes. We found that lineages with fragmented mitochondrial genomes had significantly higher rates of mitochondrial sequence evolution. In addition, lineages with fragmented mitochondrial genomes were more likely to have mitogenome gene rearrangements than those with single-chromosome mitochondrial genomes. By combining phylogenomics and mitochondrial genomics we provide a detailed portrait of mitogenome evolution across this group of insects with a remarkably unstable mitogenome structure, identifying processes of molecular evolution that are correlated with mitogenome fragmentation.
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Affiliation(s)
- Tomáš Najer
- Department of Veterinary Sciences, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
| | - Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
- Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Aleš Buček
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa, Japan
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Oldřich Sychra
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
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Kolencik S, Stanley EL, Punnath A, Grant AR, Doña J, Johnson KP, Allen JM. Parasite escape mechanisms drive morphological diversification in avian lice. Proc Biol Sci 2024; 291:20232665. [PMID: 38531401 DOI: 10.1098/rspb.2023.2665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Organisms that have repeatedly evolved similar morphologies owing to the same selective pressures provide excellent cases in which to examine specific morphological changes and their relevance to the ecology and evolution of taxa. Hosts of permanent parasites act as an independent evolutionary experiment, as parasites on these hosts are thought to be undergoing similar selective pressures. Parasitic feather lice have repeatedly diversified into convergent ecomorphs in different microhabitats on their avian hosts. We quantified specific morphological characters to determine (i) which traits are associated with each ecomorph, (ii) the quantitative differences between these ecomorphs, and (iii) if there is evidence of displacement among co-occurring lice as might be expected under louse-louse competition on the host. We used nano-computed tomography scan data of 89 specimens, belonging to four repeatedly evolved ecomorphs, to examine their mandibular muscle volume, limb length and three-dimensional head shape data. Here, we find evidence that lice repeatedly evolve similar morphologies as a mechanism to escape host defences, but also diverge into different ecomorphs related to the way they escape these defences. Lice that co-occur with other genera on a host exhibit greater morphological divergence, indicating a potential role of competition in evolutionary divergence.
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Affiliation(s)
- Stanislav Kolencik
- Department of Biology, University of Nevada Reno, Reno, NV 89557, USA
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Edward L Stanley
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Aswaj Punnath
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA
| | - Avery R Grant
- Department of Biology, University of Nevada Reno, Reno, NV 89557, USA
| | - Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana Champaign, Champaign, IL 61820, USA
- Departamento de Biología Animal, Universidad de Granada, 18071 Granada, Spain
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana Champaign, Champaign, IL 61820, USA
| | - Julie M Allen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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3
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Pedroso LGA, Klimov PB, Mironov SV, OConnor BM, Braig HR, Pepato AR, Johnson KP, He Q, Hernandes FA. Horizontal transmission maintains host specificity and codiversification of symbionts in a brood parasitic host. Commun Biol 2023; 6:1171. [PMID: 37973862 PMCID: PMC10654585 DOI: 10.1038/s42003-023-05535-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
In host-symbiont systems, interspecific transmissions create opportunities for host switches, potentially leading to cophylogenetic incongruence. In contrast, conspecific transmissions often result in high host specificity and congruent cophylogenies. In most bird-feather mite systems, conspecific transmission is considered dominant, while interspecific transmission is supposedly rare. However, while mites typically maintain high host specificity, incongruent cophylogenies are common. To explain this conundrum, we quantify the magnitude of conspecific vs. interspecific transmission in the brood parasitic shiny cowbird (Molothrus bonariensis). M. bonariensis lacks parental care, allowing the assessment of the role of horizontal transmission alone in maintaining host specificity. We found that despite frequent interspecific interactions via foster parental care, mite species dispersing via conspecific horizontal contacts are three times more likely to colonize M. bonariensis than mites transmitted vertically via foster parents. The results highlight the previously underappreciated rate of transmission via horizontal contacts in maintaining host specificity on a microevolutionary scale. On a macroevolutionary scale, however, host switches were estimated to have occurred as frequently as codivergences. This suggests that macroevolutionary patterns resulting from rare events cannot be easily generalized from short-term evolutionary trends.
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Affiliation(s)
- Luiz Gustavo A Pedroso
- Departamento de Zoologia, Av. 24-A, 1515, 13506-900, Universidade Estadual Paulista, Rio Claro, São Paulo State, Brazil.
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA.
| | - Pavel B Klimov
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Tyumen State University, 10 Semakova Str., 625003, Tyumen, Russia.
- Bangor University, Brambell 503, School of Natural Sciences, Bangor, LL57 2 UW, Wales, UK.
| | - Sergey V Mironov
- Zoological Institute of the Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Barry M OConnor
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Henk R Braig
- Bangor University, Brambell 503, School of Natural Sciences, Bangor, LL57 2 UW, Wales, UK
- Institute and Museum of Natural Sciences, Faculty of Natural and Exact Sciences, National University of San Juan, San Juan, Argentina
| | - Almir R Pepato
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - Fabio Akashi Hernandes
- Departamento de Zoologia, Av. 24-A, 1515, 13506-900, Universidade Estadual Paulista, Rio Claro, São Paulo State, Brazil
- Departamento de Ecologia e Zoologia, CCB/ECZ, Trindade, Universidade Federal de Santa Catarina, 88040-970, Florianópolis, Santa Catarina, Brazil
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Knyshov A, Gordon ERL, Masonick PK, Castillo S, Forero D, Hoey-Chamberlain R, Hwang WS, Johnson KP, Lemmon AR, Moriarty Lemmon E, Standring S, Zhang J, Weirauch C. Chromosome-Aware Phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) Elucidates Ancient Gene Conflict. Mol Biol Evol 2023; 40:msad168. [PMID: 37494292 PMCID: PMC10411492 DOI: 10.1093/molbev/msad168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Though the phylogenetic signal of loci on sex chromosomes can differ from those on autosomes, chromosomal-level genome assemblies for nonvertebrates are still relatively scarce and conservation of chromosomal gene content across deep phylogenetic scales has therefore remained largely unexplored. We here assemble a uniquely large and diverse set of samples (17 anchored hybrid enrichment, 24 RNA-seq, and 70 whole-genome sequencing samples of variable depth) for the medically important assassin bugs (Reduvioidea). We assess the performance of genes based on multiple features (e.g., nucleotide vs. amino acid, nuclear vs. mitochondrial, and autosomal vs. X chromosomal) and employ different methods (concatenation and coalescence analyses) to reconstruct the unresolved phylogeny of this diverse (∼7,000 spp.) and old (>180 Ma) group. Our results show that genes on the X chromosome are more likely to have discordant phylogenies than those on autosomes. We find that the X chromosome conflict is driven by high gene substitution rates that impact the accuracy of phylogenetic inference. However, gene tree clustering showed strong conflict even after discounting variable third codon positions. Alternative topologies were not particularly enriched for sex chromosome loci, but spread across the genome. We conclude that binning genes to autosomal or sex chromosomes may result in a more accurate picture of the complex evolutionary history of a clade.
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Affiliation(s)
- Alexander Knyshov
- Department of Entomology, University of California, Riverside, CA, USA
| | - Eric R L Gordon
- Ecology and Evolutionary Biology Department, University of Connecticut, Storrs, CT, USA
| | - Paul K Masonick
- Department of Entomology, University of California, Riverside, CA, USA
| | | | - Dimitri Forero
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogota, Colombia
| | | | - Wei Song Hwang
- Lee Kong Chian Natural History Museum, National University of Singapore, Queenstown, Singapore
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | | | | | - Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, China
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Doña J, Johnson KP. Host body size, not host population size, predicts genome-wide effective population size of parasites. Evol Lett 2023; 7:285-292. [PMID: 37475749 PMCID: PMC10355176 DOI: 10.1093/evlett/qrad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/19/2023] [Accepted: 05/18/2023] [Indexed: 07/22/2023] Open
Abstract
The effective population size (Ne) of an organism is expected to be generally proportional to the total number of individuals in a population. In parasites, we might expect the effective population size to be proportional to host population size and host body size, because both are expected to increase the number of parasite individuals. However, among other factors, parasite populations are sometimes so extremely subdivided that high levels of inbreeding may distort these predicted relationships. Here, we used whole-genome sequence data from dove parasites (71 feather louse species of the genus Columbicola) and phylogenetic comparative methods to study the relationship between parasite effective population size and host population size and body size. We found that parasite effective population size is largely explained by host body size but not host population size. These results suggest the potential local population size (infrapopulation or deme size) is more predictive of the long-term effective population size of parasites than is the total number of potential parasite infrapopulations (i.e., host individuals).
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Affiliation(s)
- Jorge Doña
- Corresponding authors: Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, United States.
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, United States.
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6
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Sweet AD, Browne DR, Hernandez AG, Johnson KP, Cameron SL. Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen. G3 (Bethesda) 2023; 13:7025741. [PMID: 36735822 PMCID: PMC10085802 DOI: 10.1093/g3journal/jkad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/16/2023] [Accepted: 01/21/2023] [Indexed: 02/05/2023]
Abstract
Sequencing high molecular weight (HMW) DNA with long-read and linked-read technologies has promoted a major increase in more complete genome sequences for non-model organisms. Sequencing approaches that rely on HMW DNA have been limited to larger organisms or pools of multiple individuals, but recent advances have allowed for sequencing from individuals of small-bodied organisms. Here, we use HMW DNA sequencing with PacBio long-reads and TELL-Seq linked-reads to assemble and annotate the genome from a single individual feather louse (Brueelia nebulosa) from a European Starling (Sturnus vulgaris). We assembled a genome with a relatively high scaffold N50 (637 kb) and with BUSCO scores (96.1%) comparable to louse genomes assembled from pooled individuals. We annotated a number of genes (10,938) similar to the human louse (Pediculus humanus) genome. Additionally, calling phased variants revealed that the Brueelia genome is more heterozygous (∼1%) then expected for a highly obligate and dispersal-limited parasite. We also assembled and annotated the mitochondrial genome and primary endosymbiont (Sodalis) genome from the individual louse, which showed evidence for heteroplasmy in the mitogenome and a reduced genome size in the endosymbiont compared to its free-living relative. Our study is a valuable demonstration of the capability to obtain high-quality genomes from individual small, non-model organisms. Applying this approach to other organisms could greatly increase our understanding of the diversity and evolution of individual genomes.
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Affiliation(s)
- Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, 2713 Pawnee St., Jonesboro, AR 72401 USA
| | - Daniel R Browne
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820 USA
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN 47907 USA
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kolencik S, Johnson KP, Grant AR, Valim MP, Kuabara KMD, Weckstein JD, Allen JM. Molecular phylogenetics of the avian feather louse Philopterus-complex (Phthiraptera: Philopteridae). Mol Phylogenet Evol 2022; 174:107556. [PMID: 35738542 DOI: 10.1016/j.ympev.2022.107556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/19/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
The avian feather louse Philopterus-complex (Phthiraptera: Ischnocera: Philopteridae) currently contains 12 genera that have been grouped together because of shared morphological characteristics. Although previously lumped into a single genus (Philopterus), more recent morphological treatments have separated the group into several different genera. Here we evaluate the status of these genera using DNA sequence data from 118 ingroup specimens belonging to ten genera in the Philopterus-complex: Australophilopterus Mey, 2004, Cinclosomicola Mey 2004, Clayiella Eichler, 1940, Corcorides Mey, 2004, Mayriphilopterus Mey, 2004, Paraphilopterus Mey 2004, Philopteroides Mey 2004, Philopterus Nitzsch, 1818, Tyranniphilopterus Mey, 2004, and Vinceopterus Gustafsson, Lei, Chu, Zou, and Bush, 2019. Our sampling includes 97 new louse-host association records. Our analyses suggest that the genus Debeauxoecus Conci, 1941, parasitic on pittas (Aves: Pittidae), is outside of the Philopterus-complex, and that there is strong support for the monophyly of a group containing the remaining genera from the complex. Some diverse genera, such as Philopterus (sensu stricto) and Mayriphilopterus are supported as monophyletic, whereas the genera Australophilopterus, Philopteroides, and Tyranniphilopterus are not. The present study is the largest phylogenetic reconstruction of avian lice belonging to the Philopterus-complex to date and suggests that further generic revision is needed in the group to integrate molecular and morphological information.
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Affiliation(s)
- Stanislav Kolencik
- Department of Biology, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557, USA.
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana Champaign, Champaign, IL 61820, USA
| | - Avery R Grant
- Department of Biology, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Michel P Valim
- Universidade Iguaçu, Nova Iguaçu, Rio de Janeiro 28300-000, Brazil
| | - Kamila M D Kuabara
- Department of Ornithology, Academy of Natural Sciences of Drexel University and Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA
| | - Jason D Weckstein
- Department of Ornithology, Academy of Natural Sciences of Drexel University and Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA
| | - Julie M Allen
- Department of Biology, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557, USA
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Boyd BM, Nguyen NP, Allen JM, Waterhouse RM, Vo KB, Sweet AD, Clayton DH, Bush SE, Shapiro MD, Johnson KP. Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites. Proc Biol Sci 2022; 289:20220042. [PMID: 35259992 PMCID: PMC8905168 DOI: 10.1098/rspb.2022.0042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Adaptive radiation is an important mechanism of organismal diversification and can be triggered by new ecological opportunities. Although poorly studied in this regard, parasites are an ideal group in which to study adaptive radiations because of their close associations with host species. Both experimental and comparative studies suggest that the ectoparasitic wing lice of pigeons and doves have adaptively radiated, leading to differences in body size and overall coloration. Here, we show that long-distance dispersal by dove hosts was central to parasite diversification because it provided new ecological opportunities for parasites to speciate after host-switching. We further show that among extant parasite lineages host-switching decreased over time, with cospeciation becoming the more dominant mode of parasite speciation. Taken together, our results suggest that host dispersal, followed by host-switching, provided novel ecological opportunities that facilitated adaptive radiation by parasites.
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Affiliation(s)
- Bret M Boyd
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Nam-Phuong Nguyen
- Department of Computer Science, University of Illinois, Champaign, IL, USA
| | - Julie M Allen
- Department of Biology, University of Nevada Reno, Reno, NV, USA
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kyle B Vo
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Sarah E Bush
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Osuna-Mascaró C, Doña J, Johnson KP, de Rojas M. Genome-Resolved Metagenomic Analyses Reveal the Presence of a Putative Bacterial Endosymbiont in an Avian Nasal Mite (Rhinonyssidae; Mesostigmata). Microorganisms 2021; 9:microorganisms9081734. [PMID: 34442816 PMCID: PMC8398770 DOI: 10.3390/microorganisms9081734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Rhinonyssidae (Mesostigmata) is a family of nasal mites only found in birds. All species are hematophagous endoparasites, which may damage the nasal cavities of birds, and also could be potential reservoirs or vectors of other infections. However, the role of members of Rhinonyssidae as disease vectors in wild bird populations remains uninvestigated, with studies of the microbiomes of Rhinonyssidae being almost non-existent. In the nasal mite (Tinaminyssus melloi) from rock doves (Columba livia), a previous study found evidence of a highly abundant putatively endosymbiotic bacteria from Class Alphaproteobacteria. Here, we expanded the sample size of this species (two different hosts- ten nasal mites from two independent samples per host), incorporated contamination controls, and increased sequencing depth in shotgun sequencing and genome-resolved metagenomic analyses. Our goal was to increase the information regarding this mite species and its putative endosymbiont. We obtained a metagenome assembled genome (MAG) that was estimated to be 98.1% complete and containing only 0.9% possible contamination. Moreover, the MAG has characteristics typical of endosymbionts (namely, small genome size an AT bias). Overall, our results support the presence of a potential endosymbiont, which is the first described for avian nasal mites to date, and improve the overall understanding of the microbiota inhabiting these mites.
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Affiliation(s)
- Carolina Osuna-Mascaró
- Department of Biology, University of Nevada, 1664 N Virginia St, Reno, NV 89557, USA
- Correspondence: (C.O.-M.); (M.d.R.)
| | - Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA; (J.D.); (K.P.J.)
- Departamento de Biología Animal, Universitario de Cartuja, Calle Prof. Vicente Callao, 3, 18011 Granada, Spain
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA; (J.D.); (K.P.J.)
| | - Manuel de Rojas
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Universidad de Sevilla, Calle San Fernando, 4, 41004 Sevilla, Spain
- Correspondence: (C.O.-M.); (M.d.R.)
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13
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Alickovic L, Johnson KP, Boyd BM. The reduced genome of a heritable symbiont from an ectoparasitic feather feeding louse. BMC Ecol Evol 2021; 21:108. [PMID: 34078265 PMCID: PMC8173840 DOI: 10.1186/s12862-021-01840-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background Feather feeding lice are abundant and diverse ectoparasites that complete their entire life cycle on an avian host. The principal or sole source of nutrition for these lice is feathers. Feathers appear to lack four amino acids that the lice would require to complete development and reproduce. Several insect groups have acquired heritable and intracellular bacteria that can synthesize metabolites absent in an insect’s diet, allowing insects to feed exclusively on nutrient-poor resources. Multiple species of feather feeding lice have been shown to harbor heritable and intracellular bacteria. We expected that these bacteria augment the louse’s diet with amino acids and facilitated the evolution of these diverse and specialized parasites. Heritable symbionts of insects often have small genomes that contain a minimal set of genes needed to maintain essential cell functions and synthesize metabolites absent in the host insect’s diet. Therefore, we expected the genome of a bacterial endosymbiont in feather lice would be small, but encode pathways for biosynthesis of amino acids. Results We sequenced the genome of a bacterial symbiont from a feather feeding louse (Columbicola wolffhuegeli) that parasitizes the Pied Imperial Pigeon (Ducula bicolor) and used its genome to predict metabolism of amino acids based on the presence or absence of genes. We found that this bacterial symbiont has a small genome, similar to the genomes of heritable symbionts described in other insect groups. However, we failed to identify many of the genes that we expected would support metabolism of amino acids in the symbiont genome. We also evaluated other gene pathways and features of the highly reduced genome of this symbiotic bacterium. Conclusions Based on the data collected in this study, it does not appear that this bacterial symbiont can synthesize amino acids needed to complement the diet of a feather feeding louse. Our results raise additional questions about the biology of feather chewing lice and the roles of symbiotic bacteria in evolution of diverse avian parasites.
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Affiliation(s)
- Leila Alickovic
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 1000 W. Cary St., Suite 111, Richmond, VA, 23284-2030, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Bret M Boyd
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 1000 W. Cary St., Suite 111, Richmond, VA, 23284-2030, USA.
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14
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Doña J, Virrueta Herrera S, Nyman T, Kunnasranta M, Johnson KP. Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites. Front Microbiol 2021; 12:642543. [PMID: 33935998 PMCID: PMC8085356 DOI: 10.3389/fmicb.2021.642543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.
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Affiliation(s)
- Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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15
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Baldwin-Brown JG, Villa SM, Vickrey AI, Johnson KP, Bush SE, Clayton DH, Shapiro MD. The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite. G3 (Bethesda) 2021; 11:jkab009. [PMID: 33604673 PMCID: PMC8022949 DOI: 10.1093/g3journal/jkab009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/13/2020] [Indexed: 01/01/2023]
Abstract
The pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.
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Affiliation(s)
| | - Scott M Villa
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, GA 30322, USA
| | - Anna I Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA
| | - Sarah E Bush
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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16
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Najer T, Papousek I, Sychra O, Sweet AD, Johnson KP. Combining Nuclear and Mitochondrial Loci Provides Phylogenetic Information in the Philopterus Complex of Lice (Psocodea: Ischnocera: Philopteridae). J Med Entomol 2021; 58:252-260. [PMID: 32829404 DOI: 10.1093/jme/tjaa166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Indexed: 06/11/2023]
Abstract
The Philopterus Complex includes several lineages of lice that occur on birds. The complex includes the genera Philopterus (Nitzsch, 1818; Psocodea: Philopteridae), Philopteroides (Mey, 2004; Psocodea: Philopteridae), and many other lineages that have sometimes been regarded as separate genera. Only a few studies have investigated the phylogeny of this complex, all of which are based on morphological data. Here we evaluate the utility of nuclear and mitochondrial loci for recovering the phylogeny within this group. We obtained phylogenetic trees from 39 samples of the Philopterus Complex (Psocodea: Philopteridae), using sequences of two nuclear (hyp and TMEDE6) and one mitochondrial (COI) marker. We evaluated trees derived from these genes individually as well as from concatenated sequences. All trees show 20 clearly demarcated taxa (i.e., putative species) divided into five well-supported clades. Percent sequence divergence between putative species (~5-30%) for the COI gene tended to be much higher than those for the nuclear genes (~1-15%), as expected. In cases where species are described, the lineages identified based on molecular divergence correspond to morphologically defined species. In some cases, species that are host generalists exhibit additional underlying genetic variation and such cases need to be explored by further future taxonomic revisions of the Philopterus Complex.
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Affiliation(s)
- Tomas Najer
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka, Prague, Czechia
| | - Ivo Papousek
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Palackeho, Brno, Czechia
| | - Oldrich Sychra
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Palackeho, Brno, Czechia
| | - Andrew D Sweet
- Department of Entomology, Purdue University, West Lafayette, IN
| | - Kevin P Johnson
- Illinois Natural History Survey, University of Illinois, Champaign, IL
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17
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Sweet AD, Johnson KP, Cao Y, de Moya RS, Skinner RK, Tan M, Virrueta Herrera S, Cameron SL. Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera. Gene 2020; 768:145312. [PMID: 33220346 DOI: 10.1016/j.gene.2020.145312] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/03/2020] [Accepted: 11/13/2020] [Indexed: 11/28/2022]
Abstract
Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.
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Affiliation(s)
- Andrew D Sweet
- Department of Entomology, Purdue University, West Lafayette, IN, USA; Department of Biological Sciences, Arkansas State University, State University, AR, USA.
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Yanghui Cao
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - 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
| | - Rachel K Skinner
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA; Department of Entomology, University of Illinois, Urbana, IL, USA
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA; Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, USA
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, USA
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18
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Kim T, Shen N, Hsiang JC, Johnson KP, Kerschensteiner D. Dendritic and parallel processing of visual threats in the retina control defensive responses. Sci Adv 2020; 6:6/47/eabc9920. [PMID: 33208370 PMCID: PMC7673819 DOI: 10.1126/sciadv.abc9920] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/01/2020] [Indexed: 05/03/2023]
Abstract
Approaching predators cast expanding shadows (i.e., looming) that elicit innate defensive responses in most animals. Where looming is first detected and how critical parameters of predatory approaches are extracted are unclear. In mice, we identify a retinal interneuron (the VG3 amacrine cell) that responds robustly to looming, but not to related forms of motion. Looming-sensitive calcium transients are restricted to a specific layer of the VG3 dendrite arbor, which provides glutamatergic input to two ganglion cells (W3 and OFFα). These projection neurons combine shared excitation with dissimilar inhibition to signal approach onset and speed, respectively. Removal of VG3 amacrine cells reduces the excitation of W3 and OFFα ganglion cells and diminishes defensive responses of mice to looming without affecting other visual behaviors. Thus, the dendrites of a retinal interneuron detect visual threats, divergent circuits downstream extract critical threat parameters, and these retinal computations initiate an innate survival behavior.
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Affiliation(s)
- T Kim
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
- Graduate Program in Neuroscience, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - N Shen
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - J-C Hsiang
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
- Graduate Program in Neuroscience, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - K P Johnson
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
- Graduate Program in Neuroscience, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - D Kerschensteiner
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Department of Neurosciences, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, Saint Louis, MO 63110, USA
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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Sweet AD, Wilson RE, Sonsthagen SA, Johnson KP. Lousy grouse: Comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host-parasite interactions. Ecol Evol 2020; 10:8379-8393. [PMID: 32788987 PMCID: PMC7417246 DOI: 10.1002/ece3.6545] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 11/08/2022] Open
Abstract
Understanding both sides of host-parasite relationships can provide more complete insights into host and parasite biology in natural systems. For example, phylogenetic and population genetic comparisons between a group of hosts and their closely associated parasites can reveal patterns of host dispersal, interspecies interactions, and population structure that might not be evident from host data alone. These comparisons are also useful for understanding factors that drive host-parasite coevolutionary patterns (e.g., codivergence or host switching) over different periods of time. However, few studies have compared the evolutionary histories between multiple groups of parasites from the same group of hosts at a regional geographic scale. Here, we used genomic data to compare phylogenomic and population genomic patterns of Alaska ptarmigan and grouse species (Aves: Tetraoninae) and two genera of their associated feather lice: Lagopoecus and Goniodes. We used whole-genome sequencing to obtain hundreds of genes and thousands of single-nucleotide polymorphisms (SNPs) for the lice and double-digest restriction-associated DNA sequences to obtain SNPs from Alaska populations of two species of ptarmigan. We found that both genera of lice have some codivergence with their galliform hosts, but these relationships are primarily characterized by host switching and phylogenetic incongruence. Population structure was also uncorrelated between the hosts and lice. These patterns suggest that grouse, and ptarmigan in particular, share habitats and have likely had historical and ongoing dispersal within Alaska. However, the two genera of lice also have sufficient dissimilarities in the relationships with their hosts to suggest there are other factors, such as differences in louse dispersal ability, that shape the evolutionary patterns with their hosts.
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Affiliation(s)
- Andrew D. Sweet
- Department of EntomologyPurdue UniversityWest LafayetteINUSA
| | | | | | - Kevin P. Johnson
- Illinois Natural History SurveyPrairie Research InstituteUniversity of IllinoisChampaignILUSA
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Osuna-Mascaró C, Doña J, Johnson KP, Esteban R, de Rojas M. Complete Mitochondrial Genomes and Bacterial Metagenomic Data From Two Species of Parasitic Avian Nasal-Mites (Rhinonyssidae: Mesostigmata). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Rodrigues ASB, Silva SE, Pina-Martins F, Loureiro J, Castro M, Gharbi K, Johnson KP, Dietrich CH, Borges PAV, Quartau JA, Jiggins CD, Paulo OS, Seabra SG. Correction to: Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources. BMC Genet 2020; 21:36. [PMID: 32209049 PMCID: PMC7092421 DOI: 10.1186/s12863-020-00842-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ana S B Rodrigues
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal.
| | - Sara E Silva
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal
| | - Francisco Pina-Martins
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal.,Centro de Estudos do Ambiente e do Mar (CESAM), DBA/FCUL, Lisbon, Portugal
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Mariana Castro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Paulo A V Borges
- Departamento de Ciências e Engenharia do Ambiente, Angra do Heroísmo, cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Açores, Portugal
| | - José A Quartau
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal
| | - Sofia G Seabra
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal
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25
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Sweet AD, Johnson KP, Cameron SL. Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice. PeerJ 2020; 8:e8759. [PMID: 32231878 PMCID: PMC7098387 DOI: 10.7717/peerj.8759] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/16/2020] [Indexed: 01/21/2023] Open
Abstract
Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.
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Affiliation(s)
- Andrew D Sweet
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, United States of America
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Doña J, Osuna-Mascaró C, Johnson KP, Serrano D, Aymí R, Jovani R. Persistence of single species of symbionts across multiple closely-related host species. Sci Rep 2019; 9:17442. [PMID: 31767919 PMCID: PMC6877549 DOI: 10.1038/s41598-019-54015-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022] Open
Abstract
Some symbiont species are highly host-specific, inhabiting only one or a very few host species, and typically have limited dispersal abilities. When they do occur on multiple host species, populations of such symbionts are expected to become genetically structured across these different host species, and this may eventually lead to new symbiont species over evolutionary timescales. However, a low number of dispersal events of symbionts between host species across time might be enough to prevent population structure and species divergence. Overall, processes of evolutionary divergence and the species status of most putative multi-host symbiont systems are yet to be investigated. Here, we used DNA metabarcoding data of 6,023 feather mites (a total of 2,225 OTU representative sequences) from 147 infracommunities (i.e., the assemblage consisting of all mites of different species collected from the same bird host individual) to investigate patterns of population genetic structure and species status of three different putative multi-host feather mite species Proctophyllodes macedo Vitzthum, 1922, Proctophyllodes motacillae Gaud, 1953, and Trouessartia jedliczkai (Zimmerman, 1894), each of which inhabits a variable number of different closely related wagtail host species (genus Motacilla). We show that mite populations from different host species represent a single species. This pattern was found in all the mite species, suggesting that each of these species is a multi-host species in which dispersal of mites among host species prevents species divergence. Also, we found evidence of limited evolutionary divergence manifested by a low but significant level of population genetic structure among symbiont populations inhabiting different host species. Our study agrees with previous studies showing a higher than expected colonization opportunities in host-specific symbionts. Indeed, our results support that these dispersal events would allow the persistence of multi-host species even in symbionts with limited dispersal capabilities, though additional factors such as the geographical structure of some bird populations may also play a role.
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Affiliation(s)
- Jorge Doña
- Department of Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Avda. Americo Vespucio 26, Sevilla, 41092, Spain. .,AllGenetics & Biology SL, Edificio CICA, Campus de Elviña s/n, 15008, A Coruña, Spain. .,Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816 S. Oak St., Champaign, IL, 61820, USA.
| | - Carolina Osuna-Mascaró
- Department of Genetics, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, Granada, 18071, Spain
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816 S. Oak St., Champaign, IL, 61820, USA
| | - David Serrano
- Department of Conservation Biology, Estación Biológica de Doñana (EBD-CSIC), Avda. Americo Vespucio 26, Sevilla, 41092, Spain
| | - Raül Aymí
- Institut Català d'Ornitologia, Museu de Ciències Naturals de Barcelona, Pl. Leonardo da Vinci, 4-5, a, Barcelona, 08019, Spain
| | - Roger Jovani
- Department of Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Avda. Americo Vespucio 26, Sevilla, 41092, Spain
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30
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Villa SM, Altuna JC, Ruff JS, Beach AB, Mulvey LI, Poole EJ, Campbell HE, Johnson KP, Shapiro MD, Bush SE, Clayton DH. Rapid experimental evolution of reproductive isolation from a single natural population. Proc Natl Acad Sci U S A 2019; 116:13440-13445. [PMID: 31182608 PMCID: PMC6613143 DOI: 10.1073/pnas.1901247116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ecological speciation occurs when local adaptation generates reproductive isolation as a by-product of natural selection. Although ecological speciation is a fundamental source of diversification, the mechanistic link between natural selection and reproductive isolation remains poorly understood, especially in natural populations. Here, we show that experimental evolution of parasite body size over 4 y (approximately 60 generations) leads to reproductive isolation in natural populations of feather lice on birds. When lice are transferred to pigeons of different sizes, they rapidly evolve differences in body size that are correlated with host size. These differences in size trigger mechanical mating isolation between lice that are locally adapted to the different sized hosts. Size differences among lice also influence the outcome of competition between males for access to females. Thus, body size directly mediates reproductive isolation through its influence on both intersexual compatibility and intrasexual competition. Our results confirm that divergent natural selection acting on a single phenotypic trait can cause reproductive isolation to emerge from a single natural population in real time.
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Affiliation(s)
- Scott M Villa
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112;
| | - Juan C Altuna
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - James S Ruff
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Andrew B Beach
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Lane I Mulvey
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Erik J Poole
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Heidi E Campbell
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Sarah E Bush
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
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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: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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32
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Bush SE, Villa SM, Altuna JC, Johnson KP, Shapiro MD, Clayton DH. Host defense triggers rapid adaptive radiation in experimentally evolving parasites. Evol Lett 2019; 3:120-128. [PMID: 31007943 PMCID: PMC6457392 DOI: 10.1002/evl3.104] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/12/2023] Open
Abstract
Adaptive radiation occurs when the members of a single lineage evolve different adaptive forms in response to selection imposed by competitors or predators. Iconic examples include Darwin's finches, Caribbean anoles, and Hawaiian silverswords, all of which live on islands. Although adaptive radiation is thought to be an important generator of biodiversity, most studies concern groups that have already diversified. Here, we take the opposite approach. We experimentally triggered diversification in the descendants of a single population of host-specific parasites confined to different host "islands." We show rapid adaptive divergence of experimentally evolving feather lice in response to preening, which is a bird's main defense against ectoparasites. We demonstrate that host defense exerts strong phenotypic selection for crypsis in lice transferred to different colored rock pigeons (Columba livia). During four years of experimental evolution (∼60 generations), the lice evolved heritable differences in color. Strikingly, the observed color differences spanned the range of phenotypes found among congeneric lice adapted to other species of birds. To our knowledge, this is the first real-time demonstration that microevolution is fast enough to simulate millions of years of macroevolutionary change. Our results further indicate that host-mediated selection triggers rapid divergence in the adaptive radiation of parasites, which are among the most diverse organisms on Earth.
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Affiliation(s)
- Sarah E. Bush
- School of Biological SciencesUniversity of UtahSalt Lake CityUtah84112
| | - Scott M. Villa
- School of Biological SciencesUniversity of UtahSalt Lake CityUtah84112
| | - Juan C. Altuna
- School of Biological SciencesUniversity of UtahSalt Lake CityUtah84112
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research InstituteUniversity of Illinois at Urbana‐ChampaignChampaignIllinois61820
| | | | - Dale H. Clayton
- School of Biological SciencesUniversity of UtahSalt Lake CityUtah84112
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33
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Doña J, Proctor H, Serrano D, Johnson KP, Oploo AO, Huguet‐Tapia JC, Ascunce MS, Jovani R. Feather mites play a role in cleaning host feathers: New insights from DNA metabarcoding and microscopy. Mol Ecol 2019; 28:203-218. [PMID: 29726053 PMCID: PMC6905397 DOI: 10.1111/mec.14581] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/15/2018] [Accepted: 03/21/2018] [Indexed: 12/31/2022]
Abstract
Parasites and other symbionts are crucial components of ecosystems, regulating host populations and supporting food webs. However, most symbiont systems, especially those involving commensals and mutualists, are relatively poorly understood. In this study, we have investigated the nature of the symbiotic relationship between birds and their most abundant and diverse ectosymbionts: the vane-dwelling feather mites. For this purpose, we studied the diet of feather mites using two complementary methods. First, we used light microscopy to examine the gut contents of 1,300 individual feather mites representing 100 mite genera (18 families) from 190 bird species belonging to 72 families and 19 orders. Second, we used high-throughput sequencing (HTS) and DNA metabarcoding to determine gut contents from 1,833 individual mites of 18 species inhabiting 18 bird species. Results showed fungi and potentially bacteria as the main food resources for feather mites (apart from potential bird uropygial gland oil). Diatoms and plant matter appeared as rare food resources for feather mites. Importantly, we did not find any evidence of feather mites feeding upon bird resources (e.g., blood, skin) other than potentially uropygial gland oil. In addition, we found a high prevalence of both keratinophilic and pathogenic fungal taxa in the feather mite species examined. Altogether, our results shed light on the long-standing question of the nature of the relationship between birds and their vane-dwelling feather mites, supporting previous evidence for a commensalistic-mutualistic role of feather mites, which are revealed as likely fungivore-microbivore-detritivore symbionts of bird feathers.
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Affiliation(s)
- Jorge Doña
- Department of Evolutionary EcologyEstación Biológica de Doñana (EBD‐CSIC)SevillaSpain
| | - Heather Proctor
- Department of Biological SciencesUniversity of AlbertaEdmontonABCanada
| | - David Serrano
- Department of Conservation BiologyEstación Biológica de Doñana (EBD‐CSIC)SevillaSpain
| | - Kevin P. Johnson
- Illinois Natural History SurveyPrairie Research InstituteUniversity of Illinois at Urbana‐ChampaignChampaignIllinois
| | | | | | - Marina S. Ascunce
- Department of Plant PathologyUniversity of FloridaGainesvilleFlorida
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFlorida
| | - Roger Jovani
- Department of Evolutionary EcologyEstación Biológica de Doñana (EBD‐CSIC)SevillaSpain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Johnson KP, Dietrich CH, Friedrich F, Beutel RG, Wipfler B, Peters RS, Allen JM, Petersen M, Donath A, Walden KKO, Kozlov AM, Podsiadlowski L, Mayer C, Meusemann K, Vasilikopoulos A, Waterhouse RM, Cameron SL, Weirauch C, Swanson DR, Percy DM, Hardy NB, Terry I, Liu S, Zhou X, Misof B, Robertson HM, Yoshizawa K. Phylogenomics and the evolution of hemipteroid insects. Proc Natl Acad Sci U S A 2018; 115:12775-12780. [PMID: 30478043 PMCID: PMC6294958 DOI: 10.1073/pnas.1815820115] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.
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Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820;
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Frank Friedrich
- Institut für Zoologie, Universität Hamburg, 20146 Hamburg, Germany
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Benjamin Wipfler
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
- Center of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Ralph S Peters
- Center of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
- Department of Biology, University of Nevada, Reno, NV 89557
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Alexey M Kozlov
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
- Institute of Evolutionary Biology and Ecology, University of Bonn, 53121 Bonn, Germany
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Karen Meusemann
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
- Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, 79104 Freiburg, Germany
- Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organisation National Research Collections Australia, Acton, ACT 2601 Canberra, Australia
| | - Alexandros Vasilikopoulos
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN 47907
| | | | - Daniel R Swanson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Diana M Percy
- Department of Life Sciences, Natural History Museum, London, SW7 5BD United Kingdom
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Nate B Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Irene Terry
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Soto-Patiño J, Londoño GA, Johnson KP, Weckstein JD, Avendaño JE, Catanach TA, Sweet AD, Cook AT, Jankowski JE, Allen J. Composition and distribution of lice (Insecta: Phthiraptera) on Colombian and Peruvian birds: New data on louse-host association in the Neotropics. Biodivers Data J 2018; 6:e21635. [PMID: 30271250 PMCID: PMC6160787 DOI: 10.3897/bdj.6.e21635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 07/25/2018] [Indexed: 11/26/2022] Open
Abstract
The diversity of permanent ectoparasites is likely underestimated due to the difficulty of collecting samples. Lice (Insecta: Phthiraptera) are permanent ectoparasites of birds and mammals; there are approximately 5,000 species described and many more undescribed, particularly in the Neotropics. We document the louse genera collected from birds sampled in Peru (2006-2007) and Colombia (2009-2016), from 22 localities across a variety of ecosystems, ranging from lowland tropical forest and Llanos to high elevation cloud forest. We identified 35 louse genera from a total of 210 bird species belonging to 37 avian families and 13 orders. These genera belong to two suborders and three families of lice: Amblycera, families Menoponidae (present on 131 bird species) and Ricinidae (39 bird species); and Ischnocera, family Philopteridae (119 bird species). We compared our bird-louse associations with data in Price et al. (2003) and recently published Neotropical studies. The majority of bird-louse associations (51.9%) were new, with most of these coming from Passeriformes, the most diverse avian order, with the most poorly known louse fauna. Finally, we found geographical variation in louse infestation and prevalence rates. With this study, we report the first comprehensive documentation of bird-louse associations for Colombia and substantially increase the known associations documented for Peru.
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Affiliation(s)
- Juliana Soto-Patiño
- Universidad Pedagógica y Tecnológica de Colombia, Tunja, ColombiaUniversidad Pedagógica y Tecnológica de ColombiaTunjaColombia
| | - Gustavo A Londoño
- Departamento de Ciencias Biológicas, Facultad de Ciencias Naturales, Universidad Icesi, Cali, ColombiaDepartamento de Ciencias Biológicas, Facultad de Ciencias Naturales, Universidad IcesiCaliColombia
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Urbana-Champaign, Champaign, IL, United States of AmericaIllinois Natural History Survey, Prairie Research Institute, University of IllinoisUrbana-Champaign, Champaign, ILUnited States of America
| | - Jason D Weckstein
- Department of Ornithology, Academy of Natural Sciences and Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, United States of AmericaDepartment of Ornithology, Academy of Natural Sciences and Department of Biodiversity, Earth, and Environmental Science, Drexel UniversityPhiladelphiaUnited States of America
| | - Jorge Enrique Avendaño
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, ColombiaLaboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los AndesBogotáColombia
| | - Therese A Catanach
- Department of Ornithology, Academy of Natural Sciences and Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, United States of AmericaDepartment of Ornithology, Academy of Natural Sciences and Department of Biodiversity, Earth, and Environmental Science, Drexel UniversityPhiladelphiaUnited States of America
| | - Andrew D Sweet
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Urbana-Champaign, Champaign, IL, United States of AmericaIllinois Natural History Survey, Prairie Research Institute, University of IllinoisUrbana-Champaign, Champaign, ILUnited States of America
| | - Andrew T Cook
- Department of Biological Sciences, University of Alberta, Alberta, Canada Department of Biological Sciences, University of AlbertaAlbertaCanada
| | - Jill E Jankowski
- Biodiversity Research Centre, Department of Zoology, University of British Columbia, Vancouver, BC, CanadaBiodiversity Research Centre, Department of Zoology, University of British ColumbiaVancouver, BCCanada
| | - Julie Allen
- Department of Biology, University of Nevada, Reno, United States of AmericaDepartment of Biology, University of NevadaRenoUnited States of America
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Sangster G, Sweet AD, Johnson KP. Paraclaravis, a new genus for the Purple-winged and Maroon-chested Ground-doves (Aves: Columbidae). Zootaxa 2018; 4461:134-140. [PMID: 30314102 DOI: 10.11646/zootaxa.4461.1.10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 11/04/2022]
Abstract
Previous molecular phylogenetic analyses and new analyses reported here demonstrate that the genus Claravis is not monophyletic and comprises two lineages, one with the species pretiosa Ferrari-Pérez, 1886 (Blue Ground-dove), and the other with two species: geoffroyi Temminck, 1811 (Purple-winged Ground-dove) and mondetoura Bonaparte, 1856 (Maroon-chested Ground-dove). Because the generic name Claravis is typified by C. pretiosa (Ferrari-Pérez, 1886), a new genus, Paraclaravis gen. nov., is described for geoffroyi Temminck, 1811 and mondetoura Bonaparte, 1856.
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Affiliation(s)
- George Sangster
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden. 2Naturalis Biodiversity Center, Darwinweg 2, PO Box 9517, NL-2300 RA Leiden, the Netherlands..
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Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD. Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 2018; 7:e34803. [PMID: 30014848 PMCID: PMC6050045 DOI: 10.7554/elife.34803] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/05/2018] [Indexed: 12/17/2022] Open
Abstract
Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified NDP as a candidate gene for this variation. Allele-specific expression differences in NDP indicate cis-regulatory divergence between ancestral and melanistic alleles. Sequence comparisons suggest that derived alleles originated in the speckled pigeon (Columba guinea), providing a striking example of introgression. In contrast, barless rock pigeons have an increased incidence of vision defects and, like human families with hereditary blindness, carry start-codon mutations in NDP. In summary, we find that both coding and regulatory variation in the same gene drives wing pattern diversity, and post-domestication introgression supplied potentially advantageous melanistic alleles to feral populations of this ubiquitous urban bird.
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Affiliation(s)
- Anna I Vickrey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Rebecca Bruders
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Zev Kronenberg
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Emma Mackey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Ryan J Bohlender
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Emily T Maclary
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Raquel Maynez
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Edward J Osborne
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research InstituteUniversity of Illinois Urbana-ChampaignChampaignUnited States
| | - Chad D Huff
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Mark Yandell
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Michael D Shapiro
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
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DiBlasi E, Johnson KP, Stringham SA, Hansen AN, Beach AB, Clayton DH, Bush SE. Phoretic dispersal influences parasite population genetic structure. Mol Ecol 2018; 27:2770-2779. [PMID: 29752753 DOI: 10.1111/mec.14719] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/15/2018] [Accepted: 04/18/2018] [Indexed: 01/01/2023]
Abstract
Dispersal is a fundamental component of the life history of most species. Dispersal influences fitness, population dynamics, gene flow, genetic drift and population genetic structure. Even small differences in dispersal can alter ecological interactions and trigger an evolutionary cascade. Linking such ecological processes with evolutionary patterns is difficult, but can be carried out in the proper comparative context. Here, we investigate how differences in phoretic dispersal influence the population genetic structure of two different parasites of the same host species. We focus on two species of host-specific feather lice (Phthiraptera: Ischnocera) that co-occur on feral rock pigeons (Columba livia). Although these lice are ecologically very similar, "wing lice" (Columbicola columbae) disperse phoretically by "hitchhiking" on pigeon flies (Diptera: Hippoboscidae), while "body lice" (Campanulotes compar) do not. Differences in the phoretic dispersal of these species are thought to underlie observed differences in host specificity, as well as the degree of host-parasite cospeciation. These ecological and macroevolutionary patterns suggest that body lice should exhibit more genetic differentiation than wing lice. We tested this prediction among lice on individual birds and among lice on birds from three pigeon flocks. We found higher levels of genetic differentiation in body lice compared to wing lice at two spatial scales. Our results indicate that differences in phoretic dispersal can explain microevolutionary differences in population genetic structure and are consistent with macroevolutionary differences in the degree of host-parasite cospeciation.
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Affiliation(s)
- Emily DiBlasi
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois
| | | | - Angela N Hansen
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Andrew B Beach
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Dale H Clayton
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Sarah E Bush
- Department of Biology, University of Utah, Salt Lake City, Utah
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sweet AD, Bush SE, Gustafsson DR, Allen JM, DiBlasi E, Skeen HR, Weckstein JD, Johnson KP. Host and parasite morphology influence congruence between host and parasite phylogenies. Int J Parasitol 2018; 48:641-648. [PMID: 29577890 DOI: 10.1016/j.ijpara.2018.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 02/04/2023]
Abstract
Comparisons of host and parasite phylogenies often show varying degrees of phylogenetic congruence. However, few studies have rigorously explored the factors driving this variation. Multiple factors such as host or parasite morphology may govern the degree of phylogenetic congruence. An ideal analysis for understanding the factors correlated with congruence would focus on a diverse host-parasite system for increased variation and statistical power. In this study, we focused on the Brueelia-complex, a diverse and widespread group of feather lice that primarily parasitise songbirds. We generated a molecular phylogeny of the lice and compared this tree with a phylogeny of their avian hosts. We also tested for the contribution of each host-parasite association to the overall congruence. The two trees overall were significantly congruent, but the contribution of individual associations to this congruence varied. To understand this variation, we developed a novel approach to test whether host, parasite or biogeographic factors were statistically associated with patterns of congruence. Both host plumage dimorphism and parasite ecomorphology were associated with patterns of congruence, whereas host body size, other plumage traits and biogeography were not. Our results lay the framework for future studies to further elucidate how these factors influence the process of host-parasite coevolution.
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Affiliation(s)
- Andrew D Sweet
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816 S. Oak St., Champaign, IL 61820, USA; Program in Ecology, Evolution, and Conservation Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, USA.
| | - Sarah E Bush
- Department of Biology, University of Utah, 257 S. 1400 E. Salt Lake City, UT 84112, USA
| | - Daniel R Gustafsson
- Department of Biology, University of Utah, 257 S. 1400 E. Salt Lake City, UT 84112, USA; Guangdong Key Laboratory of Animal Conservation and Resources, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816 S. Oak St., Champaign, IL 61820, USA
| | - Emily DiBlasi
- Department of Biology, University of Utah, 257 S. 1400 E. Salt Lake City, UT 84112, USA
| | - Heather R Skeen
- Field Museum of Natural History, Science and Education, Integrative Research Center, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA; The University of Chicago, Committee on Evolutionary Biology, Culver Hall 402, Chicago, IL 60637, USA
| | - Jason D Weckstein
- Department of Ornithology, Academy of Natural Science, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA; Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, 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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Rakitov R, Moysa AA, Kopylov AT, Moshkovskii SA, Peters RS, Meusemann K, Misof B, Dietrich CH, Johnson KP, Podsiadlowski L, Walden KKO. Brochosomins and other novel proteins from brochosomes of leafhoppers (Insecta, Hemiptera, Cicadellidae). Insect Biochem Mol Biol 2018; 94:10-17. [PMID: 29331591 DOI: 10.1016/j.ibmb.2018.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/07/2018] [Accepted: 01/07/2018] [Indexed: 06/07/2023]
Abstract
Brochosomes (BS) are secretory granules resembling buckyballs, produced intracellularly in specialized glandular segments of the Malpighian tubules and forming superhydrophobic coatings on the integuments of leafhoppers (Hemiptera, Cicadellidae). Their composition is poorly known. Using a combination of SDS-PAGE, LC-MS/MS, next-generation sequencing (RNAseq) and bioinformatics we demonstrate that the major structural component of BS of the leafhopper Graphocephala fennahi Young is a novel family of 21-40-kDa secretory proteins, referred to herein as brochosomins (BSM), apparently cross-linked by disulfide bonds. At least 28 paralogous BSM were identified in a transcriptome assembly of this species, most of which were detected in BS. Multiple additional BS-associated proteins (BSAP), possibly loosely attached to the outer and inner surfaces of BS, were also identified; some of these were glycine-, tyrosine- and proline-rich. BSM and BSAP together accounted for half of the 100 most expressed transcripts in the Malpighian tubules of G. fennahi. Except for several minor BSAP possibly related to cyclases, BSM and BSAP had no homologs among known proteins, thus representing taxonomically restricted gene families (orphans). Searching in 50 whole-body transcriptome assemblies of Hemiptera found homologs of BSM in representatives of all five families of the superfamily Membracoidea (Cicadellidae, Myerslopiidae, Aetalionidae, Membracidae, and Melizoderidae), but not in other lineages. Among the identified proteins only BSM were shared in common between all 17 surveyed leafhoppers known to produce BS. Combined CHN elemental and aminoacid analyses estimated the total protein content of BS from the integument of G. fennahi to be 60-70%.
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Affiliation(s)
- Roman Rakitov
- Paleontological Institute RAS, Profsoyuznaya St. 123, Moscow 117647, Russia.
| | - Alexander A Moysa
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow 119121, Russia.
| | - Arthur T Kopylov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow 119121, Russia.
| | | | - Ralph S Peters
- Center of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.
| | - Karen Meusemann
- University of Freiburg, Institute for Biology I (Zoology), Evolutionary Biology and Animal Ecology, Hauptstr. 1, 79104 Freiburg, Germany; Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.
| | - Christopher H Dietrich
- Illinois Natural History Survey, University of Illinois, 1816 S. Oak St., Champaign, 61820, IL, USA.
| | - Kevin P Johnson
- Illinois Natural History Survey, University of Illinois, 1816 S. Oak St., Champaign, 61820, IL, USA.
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
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Allen JM, Boyd B, Nguyen NP, Vachaspati P, Warnow T, Huang DI, Grady PGS, Bell KC, Cronk QCB, Mugisha L, Pittendrigh BR, Leonardi MS, Reed DL, Johnson KP. Phylogenomics from Whole Genome Sequences Using aTRAM. Syst Biol 2018; 66:786-798. [PMID: 28123117 DOI: 10.1093/sysbio/syw105] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 12/01/2016] [Indexed: 11/14/2022] Open
Abstract
Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes ($<$1000 Mbp) it is feasible to sequence the entire genome at modest coverage ($10-30\times$). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by annotating them with respect to the original target protein. We aligned these protein sequences with the inferred amino acids and then performed phylogenetic analyses on both the concatenated matrix of genes and on each gene separately in a coalescent analysis. Finally, we tested the limits of successful assembly in aTRAM by assembling 100 genes from close- to distantly related taxa at high to low levels of coverage.Both the concatenated analysis and the coalescent-based analysis produced the same tree topology, which was consistent with previously published results and resolved weakly supported nodes. These results demonstrate that this approach is successful at developing phylogenomic data sets from raw genome sequencing reads. Further, we found that with coverages above $5-10\times$, aTRAM was successful at assembling 80-90% of the contigs for both close and distantly related taxa. As sequencing costs continue to decline, we expect full genome sequencing will become more feasible for a wider array of organisms, and aTRAM will enable mining of these genomic data sets for an extensive variety of applications, including phylogenomics. [aTRAM; gene assembly; genome sequencing; phylogenomics.].
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Affiliation(s)
- Julie M Allen
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bret Boyd
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Nam-Phuong Nguyen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pranjal Vachaspati
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tandy Warnow
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Daisie I Huang
- Biodiversity Research Centre, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Patrick G S Grady
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Quentin C B Cronk
- Biodiversity Research Centre, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Lawrence Mugisha
- Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda.,College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, Uganda
| | - Barry R Pittendrigh
- Department of Entomology Michigan State University, East Lansing, MI 48823, USA
| | - M Soledad Leonardi
- Instituto de Biología de Organismos Marinos, Centro Nacional Patagónico, Puerto Madryn, Argentina
| | - David L Reed
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Therese A. Catanach
- Department of Ornithology Academy of Natural Sciences Drexel University Philadelphia PA USA
| | - Michel P. Valim
- Department of Ornithology Academy of Natural Sciences Drexel University Philadelphia PA USA
- Museu de Zoologia da Universidade de São Paulo São Paulo SP Brazil
- Biotério da Universidade Iguaçu Nova Iguaçu RJ Brazil
| | - Jason D. Weckstein
- Department of Ornithology Academy of Natural Sciences Drexel University Philadelphia PA USA
- 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 at Urbana‐Champaign Champaign IL USA
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46
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Light JE, Harper SE, Johnson KP, Demastes JW, Spradling TA. Development and Characterization of 12 Novel Polymorphic Microsatellite Loci for the Mammal Chewing Louse Geomydoecus aurei (Insecta: Phthiraptera) and a Comparison of Next-Generation Sequencing Approaches for Use in Parasitology. J Parasitol 2017; 104:89-95. [PMID: 28985160 DOI: 10.1645/17-130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Next-generation sequencing methodologies open the door for evolutionary studies of wildlife parasites. We used 2 next-generation sequencing approaches to discover microsatellite loci in the pocket gopher chewing louse Geomydoecus aurei for use in population genetic studies. In one approach, we sequenced a library enriched for microsatellite loci; in the other approach, we mined microsatellites from genomic sequences. Following microsatellite discovery, promising loci were tested for amplification and polymorphism in 390 louse individuals from 13 pocket gopher hosts. In total, 12 loci were selected for analysis (6 from each methodology), none of which exhibited evidence of null alleles or heterozygote deficiencies. These 12 loci showed adequate genetic diversity for population-level analyses, with 3-9 alleles per locus with an average HE per locus ranging from 0.32 to 0.70. Analysis of Molecular Variance (AMOVA) indicated that genetic variation among infrapopulations accounts for a low, but significant, percentage of the overall genetic variation, and individual louse infrapopulations showed FST values that were significantly different from zero in the majority of pairwise infrapopulation comparisons, despite all 13 infrapopulations being taken from the same locality. Therefore, these 12 polymorphic markers will be useful at the infrapopulation and population levels for future studies involving G. aurei. This study shows that next-generation sequencing methodologies can successfully be used to efficiently obtain data for a variety of evolutionary questions.
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Affiliation(s)
- J E Light
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 534 John Kimbrough Blvd., College Station, Texas 77843
| | - S E Harper
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 534 John Kimbrough Blvd., College Station, Texas 77843
| | - K P Johnson
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 534 John Kimbrough Blvd., College Station, Texas 77843
| | - J W Demastes
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 534 John Kimbrough Blvd., College Station, Texas 77843
| | - T A Spradling
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 534 John Kimbrough Blvd., College Station, Texas 77843
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47
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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48
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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: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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49
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Doña J, Sweet AD, Johnson KP, Serrano D, Mironov S, Jovani R. Cophylogenetic analyses reveal extensive host-shift speciation in a highly specialized and host-specific symbiont system. Mol Phylogenet Evol 2017; 115:190-196. [DOI: 10.1016/j.ympev.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 01/21/2023]
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50
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Rivera‐Parra JL, Levin II, Johnson KP, Parker PG. Host sympatry and body size influence parasite straggling rate in a highly connected multihost, multiparasite system. Ecol Evol 2017; 7:3724-3731. [PMID: 28616169 PMCID: PMC5468160 DOI: 10.1002/ece3.2971] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/03/2017] [Accepted: 03/16/2017] [Indexed: 11/07/2022] Open
Abstract
Parasite lineages commonly diverge when host lineages diverge. However, when large clades of hosts and parasites are analyzed, some cases suggest host switching as another major diversification mechanism. The first step in host switching is the appearance of a parasite on an atypical host, or “straggling.” We analyze the conditions associated with straggling events. We use five species of colonially nesting seabirds from the Galapagos Archipelago and two genera of highly specific ectoparasitic lice to examine host switching. We use both genetic and morphological identification of lice, together with measurements of spatial distribution of hosts in mixed breeding colonies, to test: (1) effects of local host community composition on straggling parasite identity; (2) effects of relative host density within a mixed colony on straggling frequency and parasite species identity; and (3) how straggling rates are influenced by the specifics of louse attachment. Finally, we determine whether there is evidence of breeding in cases where straggling adult lice were found, which may indicate a shift from straggling to the initial stages of host switching. We analyzed more than 5,000 parasite individuals and found that only ~1% of lice could be considered stragglers, with ~5% of 436 host individuals having straggling parasites. We found that the presence of the typical host and recipient host in the same locality influenced straggling. Additionally, parasites most likely to be found on alternate hosts are those that are smaller than the typical parasite of that host, implying that the ability of lice to attach to the host might limit host switching. Given that lice generally follow Harrison's rule, with larger parasites on larger hosts, parasites infecting the larger host species are less likely to successfully colonize smaller host species. Moreover, our study supports the general perception that successful colonization of a novel host is extremely rare, as we found only one nymph of a straggling species, which may indicate successful reproduction.
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Affiliation(s)
- Jose L. Rivera‐Parra
- Department of Biology and Whitney R. Harris World Ecology CenterUniversity of Missouri—St LouisSt LouisMOUSA
- Departamento de PetróleosFacultad de Geología y PetróleosEscuela Politécnica NacionalQuitoEcuador
| | - Iris I. Levin
- Department of Biology and Whitney R. Harris World Ecology CenterUniversity of Missouri—St LouisSt LouisMOUSA
- Present address: Department of BiologyAgnes Scott CollegeDecaturGAUSA
| | - Kevin P. Johnson
- Illinois Natural History SurveyUniversity of IllinoisChampaignILUSA
| | - Patricia G. Parker
- Department of Biology and Whitney R. Harris World Ecology CenterUniversity of Missouri—St LouisSt LouisMOUSA
- Saint Louis Zoo WildCare InstituteOne Government DriveSaint LouisMOUSA
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