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Matthews AE, Wijeratne AJ, Sweet AD, Hernandes FA, Toews DPL, Boves TJ. Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity. Syst Biol 2023; 72:802-819. [PMID: 36960591 DOI: 10.1093/sysbio/syad014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/08/2023] [Accepted: 03/21/2023] [Indexed: 03/25/2023] Open
Abstract
A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macro-evolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode vs. multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. A comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts. [Codiversification; cophylogenetics; feather mites; host switching; pooled sequencing; species delineation; symbiosis, warblers.].
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Affiliation(s)
- Alix E Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, AR, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Asela J Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Fabio A Hernandes
- Department of Ecology and Zoology, CCB/ECZ, Federal University of Santa Catarina (UFSC), Trindade, Florianópolis, Santa Catarina, Brazil
| | - David P L Toews
- Department of Biology, Pennsylvania State University, State College, PA, USA
| | - Than J Boves
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
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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: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 11/29/2022]
Abstract
The evolution of obligate parasites is often interpreted in light of their hosts' evolutionary history. An expanded approach is to examine the histories of multiple lineages of parasites that inhabit similar environments on a particular host lineage. Western North American chipmunks (genus Tamias) have a broad distribution, a history of divergence with gene flow, and host two species of sucking lice (Anoplura), Hoplopleura arboricola and Neohaematopinus pacificus. From total genomic sequencing, we obtained sequences of over 1100 loci sampled across the genomes of these lice to compare their evolutionary histories and examine the roles of host association in structuring louse relationships. Within each louse species, clades are largely associated with closely related chipmunk host species. Exceptions to this pattern appear to have a biogeographic component, but differ between the two louse species. Phylogenetic relationships among these major louse clades, in both species, are not congruent with chipmunk relationships. In the context of host associations, each louse lineage has a different evolutionary history, supporting the hypothesis that host-parasite assemblages vary both across the landscape and with the taxa under investigation. In addition, the louse Hoplopleura erratica (parasitizing the eastern Tamias striatus) is embedded within H. arboricola, rendering it paraphyletic. This phylogenetic result, together with comparable divergences within H. arboricola, indicate a need for taxonomic revision. Both host divergence and biogeographic components shape parasite diversification as demonstrated by the distinctive diversification patterns of these two independently evolving lineages that parasitize the same hosts.
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Affiliation(s)
- Kayce C Bell
- Mammalogy Department, Natural History Museum of Los Angeles County, Los Angeles, CA, USA; Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA; Zoology Department, Denver Museum of Nature & Science, Denver, CO, USA.
| | - Julie M Allen
- Department of Biology, University of Nevada Reno, Reno, NV, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - John R Demboski
- Zoology Department, Denver Museum of Nature & Science, Denver, CO, USA
| | - Joseph A Cook
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
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Grond K, Bell KC, Demboski JR, Santos M, Sullivan JM, Hird SM. No evidence for phylosymbiosis in western chipmunk species. FEMS Microbiol Ecol 2020; 96:5626339. [PMID: 31730167 DOI: 10.1093/femsec/fiz182] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks. We predicted that similarity among microbiomes increases with: (1) increasing host mitochondrial relatedness, (2) increasing host nuclear genome relatedness and (3) decreasing geographic distance among hosts. We did not find statistical evidence supporting phylosymbiosis in western chipmunks. Furthermore, in contrast to studies of other mammalian microbiomes, similarity of chipmunk microbiomes is not predominantly determined by host species. Sampling site explained most variation in microbiome composition, indicating an important role of local environment in shaping microbiomes. Fecal microbiomes of chipmunks were dominated by Bacteroidetes (72.2%), followed by Firmicutes (24.5%), which is one of the highest abundances of Bacteroidetes detected in wild mammals. Future work will need to elucidate the effects of habitat, ecology and host genomics on chipmunk microbiomes.
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Affiliation(s)
- Kirsten Grond
- Department of Molecular & Cell Biology, University of Connecticut, 91 N Eagleville Rd, Storrs, CT, 06269, USA
| | - Kayce C Bell
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave, NW, Washington, DC, 20560, USA
| | - John R Demboski
- Zoology Department, Denver Museum of Nature & Science, 2001 Colorado Blvd, Denver, CO, 80205, USA
| | - Malia Santos
- Department of Biological Sciences, University of Idaho, Life Sciences South 252, Moscow, ID, 83844, USA
| | - Jack M Sullivan
- Department of Biological Sciences, University of Idaho, Life Sciences South 252, Moscow, ID, 83844, USA
| | - Sarah M Hird
- Department of Molecular & Cell Biology, University of Connecticut, 91 N Eagleville Rd, Storrs, CT, 06269, USA.,Institute of Systems Genomics, University of Connecticut, 67 N Eagleville Rd, Storrs, CT, 06269, USA
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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: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/13/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Andrew D. Sweet
- Illinois Natural History Survey, Prairie Research Institute University of Illinois at Urbana‐Champaign Champaign Illinois
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute University of Illinois at Urbana‐Champaign Champaign Illinois
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Bell KC, Demboski JR, Cook JA. Sympatric Parasites Have Similar Host-Associated, but Asynchronous, Patterns of Diversification. Am Nat 2018; 192:E106-E119. [DOI: 10.1086/698300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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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: 0.9] [Reference Citation Analysis] [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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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: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/12/2017] [Accepted: 10/23/2017] [Indexed: 02/05/2023]
Abstract
Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g., cospeciation, host switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice. By comparing the louse and ground-dove phylogenies, we found that over long-term evolutionary scales their phylogenies were largely congruent. Many louse lineages (both species and populations) also demonstrated high host-specificity, suggesting ground-dove divergence is a primary driver of their parasites' diversity. However, the few louse taxa that are generalists are structured according to biogeography at the population level. This suggests dispersal among sympatric hosts has some effect on body louse diversity, but over deeper time scales the parasites eventually sort according to host species. Overall, our results demonstrate that multiple factors explain the patterns of diversity in this group of parasites, and that the effects of these factors can vary over different evolutionary scales. The integrative approach we employed was crucial for uncovering these patterns, and should be broadly applicable to other studies.
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Affiliation(s)
- Andrew D Sweet
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820.,Program in Ecology, Evolution, and Conservation Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820
| | - Bret M Boyd
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820.,Department of Entomology, University of Georgia, Athens, Georgia 30602
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820.,Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Scott M Villa
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Michel P Valim
- Biotério da Universidade Iguaçu, Av. Abílio Augusto Távora, 2134, RJ 26275, Brazil
| | - Jose L Rivera-Parra
- Departamento de Petroleos, Facultad de Geologia y Petroleos, Escuela Politecnica Nacional, Quito, Ecuador
| | - Robert E Wilson
- Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820
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8
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Arctic systems in the Quaternary: ecological collision, faunal mosaics and the consequences of a wobbling climate. J Helminthol 2017; 91:409-421. [DOI: 10.1017/s0022149x17000347] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
AbstractClimate oscillations and episodic processes interact with evolution, ecology and biogeography to determine the structure and complex mosaic that is the biosphere. Parasites and parasite–host assemblages are key components in a general explanatory paradigm for global biodiversity. We explore faunal assembly in the context of Quaternary time frames of the past 2.6 million years, a period dominated by episodic shifts in climate. Climate drivers cross a continuum from geological to contemporary timescales and serve to determine the structure and distribution of complex biotas. Cycles within cycles are apparent, with drivers that are layered, multifactorial and complex. These cycles influence the dynamics and duration of shifts in environmental structure on varying temporal and spatial scales. An understanding of the dynamics of high-latitude systems, the history of the Beringian nexus (the intermittent land connection linking Eurasia and North America) and downstream patterns of diversity depend on teasing apart the complexity of biotic assembly and persistence. Although climate oscillations have dominated the Quaternary, contemporary dynamics are driven by tipping points and shifting balances emerging from anthropogenic forces that are disrupting ecological structure. Climate change driven by anthropogenic forcing has supplanted a history of episodic variation and is eliminating ecological barriers and constraints on development and distribution for pathogen transmission. A framework to explore interactions of episodic processes on faunal structure and assembly is the Stockholm Paradigm, which appropriately shifts the focus from cospeciation to complexity and contingency in explanations of diversity.
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Hoberg EP, Makarikov AA, Tkach VV, Meagher S, Nims TN, Eckerlin RP, Galbreath KE. Insights on the host associations and geographic distribution of Hymenolepis folkertsi (Cestoda: Hymenolepididae) among rodents across temperate latitudes of North America. Parasitol Res 2016; 115:4627-4638. [PMID: 27630100 PMCID: PMC5104796 DOI: 10.1007/s00436-016-5255-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/07/2016] [Indexed: 11/01/2022]
Abstract
Synoptic data and an understanding of helminth parasite diversity among diverse rodent assemblages across temperate latitudes of North America remain remarkably incomplete. Renewed attention to comprehensive survey and inventory to establish the structure of biodiverse faunas is essential in providing indicators and proxies for identifying the outcomes of accelerating change linked to climate warming and anthropogenic forcing. Subsequent to the description of Hymenolepis folkertsi in the oldfield mouse, Peromyscus polionotus, additional specimens of hymenolepidids were collected or discovered in archived museum repositories from multiple species of deer mice (Peromyscus maniculatus, Peromyscus leucopus), the golden mouse (Ochrotomys nuttalli), chipmunks (Tamias striatus, Tamias amoenus), the 13-lined ground squirrel (Ictidomys tridecemlineatus), and tree squirrels (Sciurus carolinensis, Sciurus niger) from disjunct localities in the USA spanning southern Georgia, Virginia, Pennsylvania, Connecticut, the Upper Peninsula of Michigan, Wisconsin, and central Idaho. Specimens were largely consistent morphologically with the original description of H. folkertsi. Initial DNA sequence data, from a portion of the mitochondrial NADH dehydrogenase subunit 1, demonstrated intraspecific variation among three apparently geographically isolated populations attributed to H. folkertsi (uncorrected genetic distances of 2.7 % (Idaho and Michigan), 2.4 % (Virginia + Pennsylvania and Michigan), and 1.89 % (VA + PA and ID). Geography rather than host association explains the distribution and occurrence of H. folkertsi, and host colonization among deer mice, chipmunks, and other sciurids within regional sites is indicated. Genetic divergence revealed across localities for H. folkertsi suggests historically isolated populations, consistent with extended evolutionary and biogeographic trajectories among hymenolepidids and species of Peromyscus and Tamias in North America. Field inventory, that revealed these parasite populations, substantially alters our understanding of the distribution of diversity and provides insights about the nature of the complex relationships that serve to determine cestode faunas in rodents.
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Affiliation(s)
- E P Hoberg
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, USDA, Bldg 1180 BARC East, 10300, Baltimore Avenue, Beltsville, MD, USA.
| | - A A Makarikov
- Institute of Systematics and Ecology of Animals, Siberian Branch Russian Academy of Sciences, Frunze Str. 11, Novosibirsk, 630091, Russia
| | - V V Tkach
- Department of Biology, University of North Dakota, 10 Cornell Street, 58202, Grand Forks, ND, USA
| | - S Meagher
- Department of Biological Sciences, Western Illinois University, 61455, Macomb, IL, USA
| | - T N Nims
- Science Department, Perimeter College at Georgia State University, 239 Cedar Lane, 30014, Covington, GA, USA
| | - R P Eckerlin
- Mathematics, Science and Engineering Division, Northern Virginia Community College, 22003, Annandale, VA, USA
| | - K E Galbreath
- Department of Biology, Northern Michigan University, 1401 Presque Isle Ave., 49855, Marquette, MI, USA
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